The findings of both UN and Indonesian human rights investigations into the atrocities in East Timor are soon to be made public. Marian Wilkinson reports on the evidence so far.

The stench of death went straight to the back of the throat and instinctively the young woman put a cloth to her mouth. The Interfet soldier shook his head. It's worse, apparently, to try to smother the smell. A razor wire barricade and 20 odd Interfet troops held back scores of Timorese from the strip of grass leading down to the beach.

Just beyond, five empty graves lay open to a heavy sky. The exhumation was well under way. A high sheet of blue tarpaulin was strung around some poles shielding three men in army camouflage and rubber gloves from the crowd. But on the other side of the tarp, their makeshift mortuary was completely exposed. The pathologist held up a pair of rotting trousers, carefully examining the garment for holes. On the groundsheet sat a small, neat pile of bones with a skull. Beyond these sad remains, lay the next 11 graves where the diggers were still at work.

In the sweltering afternoon heat, a British police officer in a crisp white shirt, one of the United Nations civilian investigators, was already giving a briefing on the rudimentary examination.

"They are able to tell us of stab wounds, puncture holes in clothing, skull trauma, bone trauma," Detective Sergeant Steve Minhinett reported, "so they can give us fairly accurately the cause of death."

Within minutes word came from behind the tarpaulin; the first three victims had died from multiple gunshot and stab wounds.

"This will take our number through 100 in the Liquica region - that's 100 bodies," said Minhinett. "And we still have a considerable number after this."

An intense American woman in civilian clothes stepped forward. A long-time gutsy human rights activist, Sidney Jones now directs the human rights division for the UN's transitional authority in East Timor. She pointed to the empty graves. "The five bodies up here in front were buried as a result of killings on April 6 in the church compound of Pastor Rafael dos Santos. The second group of bodies are 11 over here," she turned to the beach. "These were people killed in an attack on April 17 in Dili.

"We want to find out the cause of death and whether people can identify the victims and match up physical evidence with witness testimony which we now have.

"These bodies," Jones says emphatically, "make much of the evidence amassed so far so much more credible."

On this remote beach an hour west of Dili, Jones is attempting to corroborate allegations of horrific crimes, acts that may finally be classified as war crimes committed by Indonesian-backed militias, by officers of the Indonesian army, the TNI, and by Indonesian-led police in the bloody lead-up to East Timor's independence last September.

Just how many Timorese died in the crisis and by whose order is now a matter of intense debate at UN headquarters in New York, and in Jakarta and Canberra.

Before Christmas, the Foreign Minister, Alexander Downer, attempted to revise earlier wild estimates of tens of thousands slaughtered with a more sober figure in the hundreds. But already, Canberra's revisionism is proving a little premature.

Here on the north Timor coast, the methodical work of counting the dead continues. So, too, does the investigation of who is responsible.

"One thing is certain," says Jones. "The number of reports of people being killed and the number of reported grave sites are steadily increasing. As people are becoming more confident about coming forward and reporting, the number of cases is going up."

She insists it is far too early to give an accurate death toll, but adds: "If I were to hazard a guess, I'd say somewhere between 1,500 and 2,000. That's based on very shaky data at this stage and people are going to have to accept that it's going to be a very long, slow, laborious process before we have an accurate count."

But Jones and others caution the toll could go even higher. There are still tens of thousands of East Timorese unaccounted for since September. While these figures are now believed to be the result of statistical errors, even Interfet's Major-General Peter Cosgrove says the numbers still give him some disquiet.

One thing is clear, says Jones, the known body count, about 220, is no guide to the number of victims. She knows of nearly 500 alleged killings still waiting to be investigated. The UN's transitional administration (UNTAET) is trying to determine whether these cases overlap with the several hundred cases already filed by Interfet troops or with hundreds of others the UN's civilian police investigators are working on. The figures are confounding.

But some patterns are emerging in the killings. Certain regions of East Timor, like Liquica, were hit hard. Local pro- independence figures, members of the National Council of Timorese Resistance (CNRT), were specifically targeted. Churches and priests who shielded pro-independence supporters were attacked. In many cases, TNI soldiers and police are being identified by witnesses as present at the mass killings. And, tellingly, bodies were often removed and attempts made to cover up the death toll. These patterns will be critical in determining whether a war crimes tribunal will ever be established.

Inside the razor wire barricade on the beach at Liquica is one witness who can testify to this pattern, Santiago de Santos Cencela. The bright green thongs on his feet starkly contrast with his sombre face. A few metres away, his brother Raoul is being exhumed.

Santiago's eyes flit over to the makeshift mortuary as he talks about the day he saw his brother shot dead by militia in Dili at the house of the prominent independence figure Manuel Carrascalao.

With scores of other pro-independence supporters, Santiago was sheltering at the Carrascalao home after fleeing militia attacks in the Liquica district. Hiding in the toilet he watched about 100 Thorn militia lay siege to the house. He could see TNI soldiers and police with the militia before he saw his brother shot.

The attack was reportedly ordered by Eurico Guterres, commander of the Dili militia and a vicious young criminal trained and funded by the TNI. He is now sheltering in Indonesia.

At least 12 unarmed civilians died in the attack, including Santiago's brother and Carrascalao's adopted son. The corpses were removed on trucks while Santiago, with the living, was taken to the police station. There, he recalls, he was told to sign a statement saying only one person died in the brutal attack. He refused and was held for three days.

Later, he traced the bodies of many of the victims to the mortuary and tracked them back to the Liquica district.

As he watches the UN police on the beach lay out body bags for his brother and the others, Santiago appears both depressed and gratified.

"For a long time, without the UN, we could not prove a massacre," he explains. Now he wants justice. A local militia man has been arrested in Dili, but Santiago wants the Indonesian army held accountable for his brother's murder.

"It is really important for the Timorese to show to the world that Indonesia did something very wrong here."

Inside the razor wire more Timorese are waiting. They hope to identify relatives from another massacre that took place 10 kilometres down the road from here at the church compound in Liquica. UN police are investigating the deaths of some 60 refugees, many pro-independence supporters, who were slaughtered when they sought shelter in Pastor Rafael's church.

Shot and hacked by members of the notorious Red and White Iron militia, the dead were taken away by truck, their relatives left to search for their remains.

Since Interfet's arrival, scores of rotting corpses have been discovered on the shores of a nearby lake and now on this beach.

"Unfortunately," says one UN police officer, "it's impossible to say whether they have come from the church because there are so many other reported incidents of murder in the area."

The investigation into the Liquica church massacre is significant because many eye witnesses put Indonesian military (TNI) and police at the scene.

But Sidney Jones believes proving a case against TNI officers in the massacre will be difficult.

"Certainly there is lots of testimony of the TNI giving orders from behind the militias to advance on the people inside the pastor's compound. And there is some testimony suggesting there were planning meetings before hand. But as far as I know, I'm not sure there are prosecutable cases against individual perpetrators." That is, "where they have actually tried individual cases of TNI names and identifiable murders inside the pastor's compound".

Establishing this proof is critical to the case for a future war crimes tribunal. From these junior officers, investigators need to trace the chain of command upwards to General Wiranto and his senior officers, who even today claim ignorance of the crimes committed in East Timor.

At least one UN investigator believes Western intelligence information will be essential to prove the case against senior Indonesian generals. And some classified material does exist.

Two days after the Liquica massacre, Australia's Defence Intelligence Organisation, in a secret report, blamed the Indonesian military (then still called ABRI) for failing to prevent the massacre.

"It is known that ABRI had fired tear gas into the church and apparently did not intervene when the pro-independence activists were attacked ... BRIMOB [Indonesian Police] were allegedly standing behind the attackers at the church and firing into the air ... ABRI is culpable whether it actively took part in the violence, or simply let it occur."

Whether the intelligence material is sufficiently direct in the Liquica case is debatable. Far more contentious for the Australian Government is what its intelligence services knew about the Indonesian military planning for the mass deportation, destruction and killings that took place after the UN sponsored ballot on August 30.

In the two weeks after the vote, massacres on the scale of Liquica occurred across East Timor. More than 200,000 people were transported to Indonesian West Timor, many forcibly, thousands of homes and businesses were looted and burned to the ground and major infrastructure destroyed. Under any definition, these were all war crimes. Proving a chain of command between the militias who led the rampage and the TNI high command is the central question for any tribunal.

Jones makes one telling point. As Dili burned and militias put the UN mission under siege, Wiranto declared martial law throughout East Timor on September 7. Saying he had full confidence in his forces to stabilise the situation, he stalled the push for an international peacekeeping force to occupy the territory.

But 24 hours later, two of the most chilling massacres of the crisis were carried out, with apparent TNI complicity. One is only now coming to light, a mass killing in the far western enclave of Oecussi, just a few hundred metres from the West Timor border.

In UNTAET's Dili headquarters, Superintendent Martin Davies peers over the top of his steel-rimmed glasses at the computer screen. The middle-aged British policeman with a greying beard taps quietly, scutinising the Oecussi figures as the air-conditioner blasts away the midday heat. He discourages note-taking from the large map of Timor behind him dotted with cases. It's totally unreliable, he warns.

Davies, the UN's police chief, had just returned from the mass grave site in Oecussi. Although there were rumours about the site for weeks, it was mid-December before a witness could direct the UN to the area outside a town called Passabe. The site is cut off by impassable roads and is only accessible by walking track. A 30-degree slope obscures it. "It's impossible to know how many victims are buried there," says Davies. "Figures are being bandied about that there may be 52 to 54 bodies there." But he cautions that much of the site is underground. "There are human bones and remains exposed on the surface at the moment that would give an indication there may be 10 or 12, but until the site's actually excavated we can't say," he says.

The first allegations – "something massive has occurred" – surfaced back in October. Local CNRT people have given police a long list of names, but it will may be weeks before any bodies can be identified. But Davies is in no doubt there was mass murder at the site.

The same day as these killings, when Wiranto's troops were supposedly enforcing martial law, another massacre was under way in the mountain town of Maliana. An estimated 50 people were slaughtered in the police headquarters in a district then controlled by the TNI's top ally in the pro-autonomy forces, the militia boss Joao Tavares.

The witness statements, critically, put militia, police and TNI officers present at the killings, which took place inside the police station compound and in the grounds. The victims included pro-independence activists and refugees from surrounding towns.

There are also allegations that some TNI officers had lists of names. Jones is not sure about this evidence. "There were clearly a couple of people that were targets, more well-known pro- independence figures," she explains. "But it also sounds as though it was a fairly mass killing.

"The problem is it took place in different rooms in the police station so you don't have anybody that can attest to seeing everybody killed. The testimonies we have are either from people who helped remove the bodies from the police station, or in some cases there are people who saw individuals murdered but they were taken away from the rest of the crowd."

Impeding the investigators once again is the disappearance of the victims. "We haven't found any bodies, that's the problem," Davies explains. "We've got witnesses there, and there's a figure of 53 been put on it but again ..." He shrugs. Some villagers have put the figure at 100. This pattern of cover-up points to planning and organisation which needed the complicity of TNI at a senior level.

Among East Timorese there is no debate that Wiranto and his senior commanders must be held accountable. Last May, when the UN ballot was agreed, Indonesia resisted calls for international peacekeepers coming to East Timor, insisting they would be solely responsible for security inside the territory. Now there is mounting evidence that from the time former President Habibie first proposed the ballot in January, the top commanders of the TNI worked covertly with the militias to defeat independence through violence and intimidation.

In a rambling compound, way back from the Dili waterfront, a team of East Timorese human rights investigators from the Yayasan Hak Foundation examines case studies and documents, piecing together fragmentary corroboration of the covert strategy by militias and the TNI .

The foundation's own headquarters was trashed and burned during the Dili siege and much of its work was lost. But under the guidance of a respected lawyer, Aniceto Guterres, the foundation is rebuilding its files.

Even with limited evidence, Guterres is adamant Wiranto and his commanders were ultimately responsible. "General Wiranto is involved because there is a military doctrine that says soldiers in the field have to follow orders from above. If what happened here from January to September happened without his knowledge, it meant that all these soldiers deserted from his army, it means 20,000 deserted from the army. That's impossible, The fact is General Wiranto knew."

This view has won some support from an independent Indonesian commission of inquiry into the atrocities now winding up in Jakarta.

The inquiry has targeted Wiranto's senior commanders, specifically the man who oversaw the Timor operation from Bali, Major-General Adam Damiri, and the TNI commander in Dili, Brigadier-General Tono Suratman – promoted from the rank of colonel after the crisis. The Indonesian inquiry has accused the generals of collusion in the atrocities, but the generals are strenuously denying the claims and mounting a rigorous defence.

Central to the Jakarta inquiry is evidence that the militia operations were secretly organised and funded with the assistance of senior figures in Indonesian military intelligence and the special forces, Kopassus. Indonesian reports allege these senior intelligence officers included Major-General Zacky Anwar, the one-time head of the Indonesian military intelligence service who served as the TNI's military liaison with the UN's mission during the ballot. Another was Major-General Syafrie Syamsuddin.

This analysis is also shared by Australia's Defence Intelligence Organisation, DIO. A September 9 paper on the TNI policy stated bluntly: "TNI embarked on a finely judged and carefully orchestrated strategy to retain East Timor as part of Indonesia. All necessary force was to be employed with maximum deniability ... The TNI strategy throughout has been controlled and managed from Jakarta ..."

While the TNI generals maintain their denials today, in the ruined city of Dili, two former key insiders say they have first-hand knowledge of the secret operation.

Sitting in the backyard of his brother's house, Tomas Gonsalves lights his cigarette and begins his story. Just a year ago, Gonsalves was a leading pro-Indonesian figure in Dili, a veteran who had fought with the Indonesian special forces in 1975 at Balibo where the five Australian journalists were killed. Now his weatherbeaten face tells a story of betrayal and disillusionment.

He recalls the day in late 1998 when he met Major-General Adam Damiri and Colonel Tono Suratman at the military headquarters in Dili for his first high-level meeting about the militias. Joining them, Gonsalves says, was Yayat Sudrajat, the head of the SGI, the feared intelligence task force attached to Kopassus.

The Indonesians discussed the rumoured referendum in East Timor along with secret plans to step up the training and arming of pro-Indonesia militia. Soon after, Gonsalves claims, the SGI was distributing weapons to militias throughout East Timor and he was pressured to organise the operation in his own town, the coffee growing region of Emera.

Some weeks later in March, he recalls, the SGI boss arrived in Emera with three pick-up trucks loaded with weapons for Gonsalves to distribute. Two days later he was called to a meeting with the pro-Indonesian Governor of Timor, Abilio Soares. That meeting, he says, was chilling. After discussing the security needs of the pro-autonomy front, Gonsalves claims the Governor told him that "in the near future there will be an operation throughout East Timor". As part of that operation, he claims, they were told to "kill all CNRT leaders, their families, even their grandchildren. If they sought shelter in the churches, even the Bishop's compound, we were told to kill them all, even the priests or the bishops."

Despite being shaken by this meeting, Gonsalves nevertheless agreed. But soon after a serious rift emerged between the pro- Indonesian leaders who supported autonomy in the ballot. Some were baulking over the level of violence envisaged for the campaign.

In early April, Gonsalves and other pro-autonomy leaders were summoned to Jakarta for a meeting with a senior general from Wiranto's headquarters.

According to Gonsalves's version of this meeting, Major-General Kiki Syanakhri impressed on them the need to go ahead with the militias. The TNI, said the general, "was getting weaker and the only way for the pro-autonomy forces to defend themselves is by organising the militia. If there are any sons of Timorese who wanted to fight for the red and white flag they would support them with guns and money."

Gonsalves also claims Syanakhri wanted him to take over the leadership of the militia, but the movement was split. Fearing for his own future, Gonsalves left Jakarta and went into exile in Macau.

Corroboration for Gonsalves's story comes from another insider who has recently returned to Dili. Rui Lopes, like his friend, is a former veteran of the 1975 war and fought alongside Kopassus.

The years have been kinder to Lopes. Muscle-bound and fit, he wears a gold chain with his singlet. Trucks roar into his workshop as he recounts how in late 1998, Damiri flew him to Bali to induce him to work for the pro-autonomy cause. At first, says Lopez, they wanted him to draw defectors from the independence ranks, but soon they stepped up arming and training militias. Lopes, like Gonsalves, is certain the weapons were distributed by Indonesian intelligence.

"The weapons came from [Col] Tono Suratman, he gave the green light," he says. "The SGI handed out the weapons. The Indonesians knew it was impossible to convince people to vote for autonomy, even if there was a lot of money from the central government," he explains bluntly. "By creating the militias they wanted to make them scared to vote for us."

Lopes says he had direct dealings with Major-General Zacky Anwar, the officer long rumoured to be a key figure in organising the militias. Describing Anwar as once "his good friend", Lopes claims the general organised for Damiri and the chief of military intelligence to give him 10 million rupiah to induce him to run the militias.

Lopes went to the Jakarta meeting with Gonsalves that April and confirms the split in the pro-Indonesian ranks. But when Gonsalves fled, Lopes returned to Dili, gathering information and passing it through intermediaries to CNRT. He distanced himself from the militia killings, but kept his contacts with senior Indonesian generals.

In August, when it was clear the independence cause was surging, Lopes claims Anwar advised him to set up a home base in Indonesian West Timor because they would need to launch a guerilla war to hold the territory. "The Indonesian army had its hands and legs tied in front of the international community," he recalls the general telling him. "If autonomy was rejected they would prepare for a guerilla war in [the western towns of] Atambau, Balibo and Suai."

The testimony of these two insiders is extremely significant, but on its own not enough for a case against the generals, Jones warns.

The key question is whether any of these meetings and plans can be tied to individual deaths. "My own feeling is that you do what you can with low-ranking TNI soldiers, bring those cases forward," Jones advises. "I don't think you can start with the top and work down. I don't think you're going to get evidence that will stand up in court until you have some of these specific cases with much lower ranking officers actually prosecuted and brought out in the open."

One such case now under intense scrutiny is the horrific massacre in the western coastal town of Suai. On September 6, as Australia and the world stumbled to respond to the Timor crisis, 100 unarmed Timorese civilians, maybe more, were slaughtered in the Suai church compound in a militia attack. Again, TNI and police were present. Among those killed was a prominent Timorese priest, Father Hilario Modeira, along with two of his colleagues. For both UN and Indonesian investigators, much is at stake in the case.

In a ransacked building in the mountains, a safe distance from the terrifying memories of Suai, a young boy sits in a white plastic chair, his feet just touching the floor. Until last September, Toto lived down in Suai with his cousin, Father Hilario, supported by the priest's generosity. As Father Hilario's brother waits outside, Toto says he wants to talk about the day "Papa Saint" died.

It was about two in the afternoon, the boy recalls, when he first heard the shooting. All day, Father Hilario had tried to telephone the police and army headquarters but no-one would answer. One person he could reach was Bishop Belo up in Dili. He told his priest to pray.

Toto describes how people began running everywhere as the shooting went on and on. He hid in Father Francisco's bedroom, he said. He wanted to see Father Hilario on the veranda, but others hiding with him warned him to stay down. Then he heard a shot and Father Hilario fell. "He lay down on the veranda saying please, please, help me, and called out Father Cico's name," Toto says. "Then he died."

When the killings were over, the boy and six others huddled in the bedroom until the compound was set on fire. Men began searching the house so they fanned the smoke to screen themselves. When it was quiet, the frightened survivors made their escape. "I had to walk over the dead bodies," the boy says. "I think there were a lot of people but I didn't count them."

Down in UN police headquarters in Dili, Sergeant Sue King is drawing a rough diagram of the Suai compound, trying to explain why the killing went on for four hours. The militia, it seems, were searching the compound. The killing, she believes, was "on and off – there are a lot of places to look for people". She indicates hiding places.

For several weeks, King, a young Australian Federal Police officer from Sydney, has been piecing together evidence on the Suai massacre. In the months before the ballot, the church compound was a refuge for thousands of pro-independence supporters who had been driven from their homes by militias. Father Hilario's courage in sheltering the refugees, and that of his colleagues, Father Francisco Soares and Father Tarcisius Dewanto, brought the attention of US senators and the international media, but it infuriated the local TNI commander and the militia.

On September 4, when the UN announced the overwhelming vote for independence, the priests knew they were sitting targets. Fearing the worst, Father Hilario urged thousands of refugees to leave the compound, but some were too frightened to go.

From witness statements, Sergeant King now thinks about 400 unarmed people were left in the compound when the militia surrounded them. Her best estimate, she says, is that some 100 people were slaughtered. Others put the figure higher.

The wet season hasn't helped her inquiries. "Interfet didn't investigate till much later and with the rain, that crime scene was severely contaminated." But what evidence remained spoke clearly of a massacre – blood stains and a pile of empty cartridge shells.

"There was evidence of gunfire to the walls, all from semi- automatic rifles," she says. A dozen burnt corpses also remained, but, as with other massacre sites, most of the bodies had been removed by truck.

It was the Indonesian human rights inquiry that announced the discovery of Father Hilario's body last November. Three graves were found 20 kilometres from Suai, on the Indonesian side of the border, that held the remains of the priests and 23 unidentified victims. The Indonesian forensic pathologist listed the cause of death as shooting in the case of Father Hilario and Father Tarcisius. Father Francisco had died when his throat was slashed. All three priests were buried in a single grave.

The find was a major breakthrough for the Indonesian inquiry, the first victims discovered on Indonesian soil. The discovery boosted the credibility of the Indonesian inquiry into the atrocities, but East Timorese human rights activists and the UN's Jones remain sceptical. They fundamentally doubt whether any Jakarta inquiry will lead to high-level convictions.

They point out that the Indonesian inquiry is a fact-finding exercise with no power to prosecute. Jones is convinced the Wahid Government supported it to forestall an international tribunal and believes that is still the Government's thinking.

"If they were able to show that they were achieving anything substantial this would effectively constitute the domestic remedy which would make any international prosecutions superfluous," she claims.

The UN human rights panel on the Timor atrocities has recently completed its investigation. It was specifically advised to co- operate with Jakarta's inquiry. Its report is now with Secretary-General Kofi Annan, who is expected to release it soon.

Jones, who has not been shown the report, says the recommendations range from an international court with Timorese and Indonesian judges, to "border courts" set up under Indonesian law and Indonesian judges with some international participation.

But she is dubious about the ultimate success of any high-level Indonesian prosecutions.

Despite the undoubted courage and determination of the current Indonesian human rights inquiry, the Indonesian court system is another matter. "I'm not frankly sure about whether any court in Indonesian will succeed ... in bringing people to justice," she says, "or whether you can get completely impartial judges in a legal system which, even given the democratic changes, is marked by a huge degree of corruption, politicisation and lack of professionalism."

While most local observers agree that militia members should be tried in East Timorese courts, the prosecution of the Indonesian command remains the issue at stake. For the thousands of East Timorese who lost relatives, friends, their homes, jobs, businesses and their political future, the Indonesian commanders must stand trial.

Sitting in a ransacked office in his home town, Father Hilario's brother, Louis, presses his hands to his face. As he fights back tears, he demands justice for his family. His father and two brothers were killed under Indonesian occupation. His job is gone, his friends in this town are dead, the local woman who worked for the UN mission was raped and murdered, hundreds of lives destroyed. He calms his weeping by lighting a cigarette.

The Indonesian army must be held responsible, he believes. He is prepared to wait for a war crimes tribunal, but it must come. "It is not a problem if we have to wait one or two years, but we want justice in the end," he says. "It will break the hearts of the Timorese if there is no justice."