Marian Wilkinson – Indonesian security forces drew up extensive plans weeks before the United Nations ballot to move 200,000 people from East Timor using thousands of trucks and escort vehicles and marking out road, air and sea routes, Indonesian documents show.

The documents, obtained by the Timorese human rights organisation Yayasan Hak, include a police report dated August 1999 showing that mass evacuations were planned whichever side won the ballot.

While the plans purported to be for the evacuation of foreigners and those who supported the pro-autonomy cause, the massive numbers in the report indicate that forced deportations were inevitable.

But neither the scale of the deportations nor the level of violent destruction that followed the ballot was predicted by Australia's intelligence agencies.

On August 30, just five days before the mass evacuations and widespread violence, a secret Defence Intelligence Organisation (DIO) report advised the Government that the "form and extent" of the violence in East Timor would remain "predictable at least for the next few weeks".

As a result of this analysis, the intelligence agency put the security "watch condition" on Timor at below the highest crisis level, advising that "the East Timor warning problem remains at Watch Condition 3" – described as "below those seen in more anarchic conflicts". It concluded that a higher watch condition "could be necessary by October".

Five days after this report, on September 4, the UN announced the ballot result showing that nearly 80 percent of the country had voted for independence. Within hours Indonesian security forces began mass evacuations, including thousands of forced deportations.

This was accompanied by widespread killings and the burning and looting of towns by militias, often in the presence of Indonesian security forces.

But 24 hours before this crisis exploded, the DIO was still unclear about the Indonesian strategy. While the agency was aware of Indonesia's plans to evacuate its supporters if independence won, it was apparently unaware of the mass deportation about to be launched.

On September 3, the DIO reported that "contingency evacuation plans ... encompassing the evacuation of foreigners as well as Indonesian citizens, are being developed", but nowhere did the report suggest that forced deportations were to begin a day later.

The agency did correctly predict a surge in violence, including possible attempts to murder key independence figures and foreigners. But in a "key judgment", its report on September 3 stated that "civil war or widespread disorder is not a foregone conclusion ...".

The DIO analysis was passed to Australia's allies, including the US, Britain, Canada and New Zealand. By then, armed militias were already erecting roadblocks throughout Dili, terrorising Timorese and driving foreigners from the countryside.

In an extensive interview on the crisis, the Foreign Minister, Mr Downer, acknowledged that the Government did not predict either the mass deportations or the scale of the violence, but he does not believe there was an intelligence failure.

"The evacuation of people in the way they did it surprised me," he told the Herald. "The fact that it happened at all surprised me. And the motive for it to this very day is not entirely obvious."

According to Mr Downer, in the months before the ballot the Government and the intelligence services were bombarded by allegations and documents which were examined and judged for their authenticity.

At the same time, officials were trying to filter out deliberate deception by some senior Indonesian figures, including military commanders.

One Indonesian document widely leaked in July had revealed plans to evacuate its supporters and the destruction of facilities. But this report – called the Garnadi document after its author – was rejected as false by the Indonesian Government.

"The Indonesians ran two basic lines," Mr Downer said. "One of them was that the documents could be false ... the second was this was just produced by some low-ranking person and doesn't have the authority of the Indonesian hierarchy."

But other information pointing to the inevitable crisis was available. A report by the UN mission in East Timor shows that on August 17 the UN had "persistent reports" from officials in the western district of Bobonaro that after the ballot roadblocks would be set up, the electricity would be cut, "retribution attacks" against pro-independence people would begin and autonomy supporters would be evacuated to West Timor. Those refusing to go "will be killed".

Yet when the killings and deportations began, the Australian Government was taken by surprise and Mr Downer agreed that its agencies did not warn that the crisis would escalate as dramatically as it did.

"The level of violence came as a surprise to me," he said. "That people were deported [came] as a surprise to me and obviously at the time we were talking to the Indonesians constantly about what was going on and their explanation was these people were being moved out for their own security."

Mr Downer also revealed that Australia and the US had heard reports of "a scorched earth" plan for after the ballot but the Government made a judgment that it was not the most likely outcome.

Mr Downer said: "Let us say you have a spectrum of 0 to 10, 10 just a complete massacre of the population. What happened was about eight ... our expectations were around five. That's an on-balance judgment and it was therefore a little worse that we had expected."

But he believes that despite this, there was no failure by the Government or its agencies because there were contingency plans for all possible outcomes – including the violence that eventually erupted.

"We were prepared for everything [and] we proved that. We were even prepared for a worse situation than actually occurred; what, for example, we would have done if they started killing people in the United Nations compound, we had contingency plans for that sort of thing." As a result, Mr Downer concluded: "There wasn't a failure on anybody's part."

But while the contingency plans for evacuating Australians and other foreigners, including the UN mission, were extremely effective, it left the Timorese exposed to the militias and the Indonesian security forces until Jakarta agreed to an Interfet force.

In the intervening weeks, hundreds, perhaps thousands, of Timorese were slaughtered and the country virtually destroyed.

The Opposition Foreign Affairs spokesman, Mr Laurie Brereton, has long criticised the Government's Timor policy and called for a reassessment, but he has been ignored by the Government.

Now a number of Australian defence academics are joining the calls for a broad inquiry into the Government's Timor policy, including its intelligence analysis.

"There was a failure," the prominent Indonesian specialist Mr Bob Lowry told the Herald. A visiting fellow at the Australian Defence Force Academy (ADFA) and a former military attache in Jakarta, Mr Lowry believes the raw material to predict the crisis was available. "What was lacking was an analysis of the situation."

He believes the Government and the intelligence agencies should undertake a critical review of their actions and produce a public report. "I think if the bureaucracy doesn't take this opportunity there is something wrong with the way it operates."

He is joined by a fellow ADFA academic, Dr Peter Bartu, who served on the UN mission in Timor throughout the ballot and saw the crisis develop.

Dr Bartu believes the Government is in denial over the failings of the Timor policy. He says there should be a broad-ranging review of the policy and the crisis management during 1999.

The raw material pointing to the inevitable climax was available, he said, but because many of the sources were East Timorese activists, church organisations or human rights groups, it was discounted.

Significantly, before the final crisis erupted, the DIO analysis of the violence in Timor had proved largely accurate, judged by copies of its reports leaked to the media during 1999.

It sheeted the blame for the violence home to senior Indonesian generals even while the Australian Government took a more diplomatic position publicly.

On September 9, after the crisis erupted, a DIO assessment spelt out what the Australian Government had not said publicly throughout the ballot – that the TNI (Indonesian military) had used "all necessary force" with "maximum deniability" to retain East Timor as part of Indonesia. And it stated bluntly that "the TNI strategy throughout has been controlled and managed from Jakarta".

But the analysis also persisted in the claim that the evacuation plan, Operation Wira Dharma, was switched to a deportation plan only after the vote when the UN mission "began to buckle".

This, according to Timorese refugees and former TNI soldiers, was a fundamental misjudgment. "The big sweep", as the Timorese called it, was increasingly discussed by even junior officers at least two weeks before the ballot.

A document discovered in the rubble of military headquarters by Yayasan Hak appears to be the original Operation Wira Dharma plan. While it does read as an evacuation plan for autonomy supporters its intelligence plan, significantly, defines all pro-independence political activists as "enemy troops".

In a telling section, it says: "The enemy troops are the community groups of East Timor who are against integration with Indonesia." They are listed as the CNRT (the National Council for Timorese Resistance), the solidarity council of students, and the youth organisation of East Timor.

When the big sweep was launched, many pro-independence Timorese had no choice in their evacuation. Militias, backed by the TNI and police, burnt their homes and destroyed services, leaving them as refugees. Anyone staying behind was deemed to be "an enemy", exposing them to possible death. By then, the UN was under siege in its Dili compound, leaving them with no international protection.