Last week was the fifth anniversary of the independence vote in East Timor and the Indonesian atrocities that followed. At the time of the killings there was an international uproar and some confidence that the perpetrators would be prosecuted. That confidence has now turned to dust. As promised, Indonesia put its own military on trial. But one by one, they have all walked free, except for one man, Abilio Soares, the former governor of East Timor. His imprisonment just a few weeks ago marks a miserable end to the quest for justice. Mark Davis met with him in Jakarta's Cipinang prison.

Reporter: Mark Davis

One of Jakarta's most democratic institutions is Cipinang prison. It takes all comers – corrupt businessmen and politicians, the Bali bombers, rapists, fraudsters and murderers. Anyone can get in here – anyone that is, except those who murder, rape and torture East Timorese. For them, it seems these gates will never be prised open.

Abilio Soares is in shock. After five years of impressive-looking trials and hearings, he has just become the only person to be imprisoned for crimes against humanity in East Timor.

Abilio Soares, former governor of East Timor (Translation): If human rights violations occurred who is responsible?

Indonesia's former governor in East Timor has become something of a martyr in political circles here since he was set to Cipinang in July. A loyal servant of Jakarta, rewarded with a jail cell for doing what was asked of him.

Mark Davis: Do you feel betrayed by people who were your friends, who supported you when you were supporting Indonesia? Do you feel betrayed that...?

Abilio Soares (Translation): I don't feel betrayed by the people but by the government.

No television interviews with Abilio have been allowed but I managed to speak with him in Cipinang as he met with his legal team, preparing one last appeal, and it seems he no longer feels obliged to protect his former friends in the Indonesian Government and military.

Abilio Soares (Translation): I didn't help them to kill people. You can see here that I did not form the militia and neither did I support them.

This week, five years ago, East Timor was being burnt to the ground and its people massacred. The Timorese had just spurned Indonesia at the referendum. It was a fittingly brutal end to Indonesian rule.

In its first year, the newly independent East Timor seemed more like a huge crime scene than a nation. The country was awash with evidence of the murders and massacres that had occurred there with the complicity of the Indonesian military. To avoid the growing call for an international criminal tribunal, the Indonesian Government struck a deal with the UN.

Indonesia would prosecute its own military, police and officials. It seemed like a bad joke at the time. And now, five years later, the punch line has been delivered – just one fall guy, and an East Timorese one at that.

Soares no longer feels obliged to mince his words about who he holds responsible for the atrocities of '99 – not the militias, but the local police chief and in particular, the Indonesian military commander based in Dili.

Abilio Soares (Translation): Indeed, he should be punished, because I shouldn't be the one here. It should be Tono Suratman.

Tono Suratman was 1 of 21 military and police officers that Indonesia claimed would be prosecuted for abuses in East Timor. All of them walked free. At his hearing, Suratman was cleared of responsibility for a wave of killings, in particular two appalling massacres in early '99, five months before the referendum, massacres for which Abilio Soares was held responsible.

Mark Davis: Do you now accept any responsibility for those killings?

Abilio Soares (Translation): I think the killings were carried out by armed men. The people bearing arms, either legally or illegally, were the security forces, not the governor. That wasn't the governor's role. The people with weapons who would oppose those using arms, were the defence forces, either the police or the army.

From the beginning of '99, militias began terrorising remote villages far from public scrutiny, forcing people to join, torturing or murdering those who refused to do so.

Man (Translation): If you'd been there last night, you'd be dead now.

Man 2 (Translation): Did the head of the village die?

Man (Translation): Yes, he died.

The more they killed, the more money they received, and the more outrageous they and their friends in the army became.

Hospital worker (Translation): Who do you think shot you?

Patient (Translation): It was... the Indonesian troops.

Hospital worker (Translation): The troops. You saw the troops.

In early April, together with Indonesian troops, they surrounded a church in Liquica suspected of harbouring independence supporters, and opened fire, hacking to death anyone who tried to escape.

On April 17, the militias made their first direct assault upon the capital Dili, starting with a rally outside the office of governor Abilio Soares.

Until this day, Dili had been free of militia massacres. Victims from the rural areas were seeking refuge in the capital, about 150 of them camping in the house and gardens of Manuel Carrascalao – a wealthy and influential protector. Most of them had already suffered terribly at the hands of the militias and all of them could hear the speeches coming from outside the governor's office just a stone's throw away.

Rally (Translation): I take this opportunity to order all militia, both ordinary soldiers and commanders, from April 17 onwards, to seek them out, capture them... If they resist, shoot them dead.

Mark Davis: Everybody knew they were going there to kill them so that means that people in responsibility should have taken responsibility?

Abilio Soares (Translation): But who supplied those weapons? And who supervised their use? That isn't the governor's responsibility. And to let you know... when they rallied in front of the governor's office, which resulted in killing of Manuel Carrascalao's son, I did not agree to their rallying. At the time, I didn't agree to it and did not attend the rally.

The mob descended upon the Carrascalao house. With high fences surrounding the building, there was no escape. They were butchered in the middle of Dili as police and army stood by and their commanders ate their lunch.

12 bodies were recovered including Manuel Carrascalao's son. Witnesses believe there were dozens more killed. 40 are still missing.

Mark Davis: Where were you when the killings were happening at the Carrascalao house? Where were you?

Abilio Soares (Translation): I was at the governor's office. I was at the governor's residence at the time receiving the Foreign Minister's delegation from Northern Ireland.

Translator: When it happened he was a guest from...

Mark Davis: The lunch, the lunch. Yes. And what did you do when you heard the killings were happening?

Abilio Soares (Translation): I received a phone call when the killings happened, about an incident at the Carrascalao house. I instructed the head of my department to contact the security forces to handle the situation. If I am not mistaken, the police arrested 20 people.

Mark Davis: Well, it was a terrible massacre, helpless refugees, you know, nowhere to run. Someone should be in jail for that. Who should be in jail for that?

Abilio Soares (Translation): At the time this involved supporters and opponents. Those 20 people who were arrested should be tried. Where are they now?

Mark Davis: Where were the police and where were the army when the mob was going down with machetes to kill the people? Where was the police and where were the army?

Abilio Soares (Translation): Well, that's a good question. Where were the security forces at the time?

Where were the security forces is the key question that could be asked for all of '99 and it's not hard to answer. The police or army were present at virtually every major atrocity of that year, sometimes directly involved in the killings, more often literally standing back and watching as the militias were sent in, militias which, according to Soares, they directed and controlled.

Abilio Soares (Translation): I feel that they are the ones who should be here. I should be free. They were the ones responsible for security.

Mark Davis: Instead of you? Why? Why?

Abilio Soares (Translation): Because under the 5 May agreement, security for the referendum was given to the military and police.

Mark Davis: Well, who else should be here? Should General Wiranto be here instead of you? Should Adam Damiri be here instead of you?

Abilio Soares (Translation): Yes, Adam Damiri was Tono Suratman's superior.

So they are the ones who should be held accountable for the human rights violations in East Timor because they were responsible for security, not me.

Abilio's defence has a familiar ring to it – it's the defence of every government man under every military regime. And it's not a bad defence.

But in East Timor, government officials were hardly arm's length from the mad plans of the Indonesian military and, according to this former Indonesian sympathiser, neither was Abilio Soares.

Tomas Goncalves (Translation): On March 26 the Governor told us that from May 1, throughout the territory, we were to liquidate all the CNRT members, down to their grandchildren. If the people sought help from priests, nuns or the bishop, these too should be killed.

Mark Davis: Tomas Goncalves has accused you, though, of pulling all the integration leaders together and giving instructions that all the CNRT people will be killed from May 1, down to their grandchildren.

Abilio Soares (Translation): I ask for proof. I ask for the proof.

Because that never happened. That never happened.

Mark Davis: It's hard to prove, I guess, but it is an accusation he's made that, in March, you said that all the CNRT people would be killed from May.

Abilio Soares (Translation): By whom?

Mark Davis: Tomas Goncalves. You don't know Tomas Goncalves?

Abilio Soares (Translation): I know. Who did you say is going to carry out the killings?

Mark Davis: The militias, the militias, not you, not you – no, you're a government man.

There were lots of government men in Dili and Jakarta involved in 1999, all of whom apparently argued their case better or had better friends to argue it for them than Abilio Soares did. None of them were charged.

Mark Davis: Where did the money come from? Who financed the militias...

and the FPDK?

Translation: He never been supported. He doesn't know. He doesn't have a notion. No idea? No idea, yeah.

Witnesses had detailed the involvement of ministers, like Yunis Yosfiah, officials from Ali Alatas's foreign affairs department and the current head of Indonesian intelligence, Hendropriyono, in heavily funding the biggest pro-Indonesian lobby group in East Timor, the FPDK. Many government officials in East Timor joined the daintily named Forum for Peace, Democracy and Unity. Abilio now has a rather blunt assessment of what the FPDK really was.

Mark Davis: You knew all the FPDK people. You'd go to their meetings.

You know them all, yeah?

Abilio Soares (Translation): Yeah.

Mark Davis: Now, you know they were leaking money to the militias so you must have questioned how did the FPDK get money.

Abilio Soares (Translation): The FPDK was under the army. I've written it down.

Translator: I mean the associates of the military.

Mark Davis: Associates of the military?

Abilio Soares (Translation): At the time the militia were the military arm of the FPDK.

And the FPDK was funded by prominent Jakarta ministers – now, that would make an interesting court case. And the money trail to Jakarta doesn't end there, as various former public servants in Dili have told.

Mark Davis: So they turned your department into a bank for the militia?

Former public servant (Translation): It was all for the militia. That whole 1999 budget was for the militia alone.

From the rubble of government offices, emerged instructions directly from Abilio authorising development and welfare funds to be diverted for the socialisation of autonomy, supposedly a kind of education program for the referendum.

Government worker (Translation): The penggalangan, which means militia activities,

Abilio Soares (Translation): On the issue of socialisation of autonomy, as part of the Indonesian government, that is something I had to do. And that was my responsibility as governor. The socialisation of autonomy is not the same as murder. It isn't so.

Abilio Soares – the man in the middle. Neither one of the military masterminds nor one of the machete-wielding thugs who turned against him in the end.

Abilio Soares (Translation): Because even my family and I were subject to their aggression.

One man – the end result of a grand-sounding quest that was to deliver justice for the dead and a lesson to military commanders everywhere.

One wonders what lessons the rest of the class of '99 drew from the experience.

Militia leader Eurico Gutteres was convicted, but is free pending an appeal and now works for the ruling party in Indonesia, Megawati Sukarnoputri's PDI.

After Tono Suratman was acquitted, he was promoted to the position of Brigadier General. His superior officer, Adam Damiri, failed to appear at the tribunal four times. He was busy running the bloody war against separatists in Aceh. When he finally fronted, he, too, was acquitted.

Timbal Silaen, the chief of police in East Timor in '99, was also acquitted of crimes against humanity. He has now been appointed police chief in West Papua, a province undergoing its own wave of terror at the hands of Indonesian forces. And the ultimate military commander of '99, General Wiranto, is now pursuing his post-military career – entertainer, politician, businessman. Wiranto has also been indicted for crimes against humanity, but it's unlikely his case will ever be heard. A bizarre end to a very sordid tale.

That story co-produced by East Timorese journalist Jose Belo. And just yesterday the East Timorese Government called for Soares to be released as part of its reconciliation process.