Newly published intelligence documents, declassified by the US, shed new light on the turbulent events surrounding the 1999 independence referendum in Timor Leste, when Indonesian-backed militia gangs went on a murderous rampage across the country.

Key points: Declassified documents suggest Australia did not support or plan for a peacekeeping mission in Timor Leste until the last minute

Declassified documents suggest Australia did not support or plan for a peacekeeping mission in Timor Leste until the last minute Then foreign minister Alexander Downer rejects the claims, saying Australia never lobbied against a peacekeeping force

Then foreign minister Alexander Downer rejects the claims, saying Australia never lobbied against a peacekeeping force Former PM John Howard said for years that the "liberation" of Timor Leste was one of his proudest achievements

The documents back claims that it was the US — and not Australia — that ultimately forced Indonesia to accept peacekeepers into the country and uphold the referendum result, where an overwhelming 78.5 per cent of Timorese voted for independence.

They also suggest Australia did not support or plan for a peacekeeping mission until the very last minute, and only after the US had succeeded in forcing Indonesia to respect the independence vote and stop the escalating violence by pro-integration militias against the Timorese people.

Nowhere in the documents is there any sign that Australia actively pressured the US to take steps to protect the Timorese, despite the worsening violence and evidence that Indonesia's armed forces were supporting or even working alongside the militia groups.

Documents dispel narrative on Timor Leste 'liberation'

The claims are among hundreds, if not thousands of pages of declassified cables, intelligence reports and other documents published this week by the National Security Archive, ahead of Friday's 20th anniversary of the independence referendum.

The intelligence documents serve to dispel the Federal Government's own narrative that has receded anyway over the past decade.

For years after the referendum, John Howard maintained that the "liberation" of Timor Leste was one of his proudest achievements as prime minister, alongside the gun buyback scheme.

But the archive documents show in reality it was the US that succeeded in pressuring Indonesia to "pull back from the brink of disaster" and allow a multinational peacekeeping force into the country, as militia gangs continued to massacre Timorese with impunity.

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The US documents add new context to Australian diplomatic and intelligence cables leaked in late 1999 showing that despite Mr Howard's later claims, Australia had consistently lobbied against the deployment of peacekeepers.

One CIA report in the newly published US documents shows that it was well-known that Indonesia's military was supporting the murderous militias.

"Jakarta's initiatives to control the security situation in East Timor have had little impact because Indonesian military elements have supported pro-integration militias," read an article in the CIA's Terrorism Review.

"Numerous reports indicate that Indonesian military elements have aided or worked with pro-integration militias. The Indonesian military on September 6 worked openly with the militia to force people out of East Timor."

Downer says 'assertions are totally wrong'

The CIA report directly contradicted comments by Australia's then foreign minister Alexander Downer, who throughout 1999 had downplayed the role of the Indonesian armed forces (TNI) and claimed only "rogue elements" of the TNI were responsible for the violence.

Alexander Downer said Australia made a "huge effort" to stem violence in Timor Leste, including a summit with president BJ Habibie. ( Reuters: Enny Nuraheni )

But in a response to the ABC when asked if the US and not Australia had forced Indonesia to accept peacekeepers, Mr Downer rejected the claims.

"I haven't time to read all those documents but your assumptions are plain wrong," he said.

"There is a long record of Australian commentary on these events — we never lobbied against a peacekeeping force and you seem totally unaware of the huge effort we made in 1999 to stem the violence in East Timor — including the Bali summit with president [BJ] Habibie.

"The assertions you make are totally wrong.

"And as for the Americans, perhaps you are unaware of the difficulty we had in getting Clinton and Berger engaged to help at any stage."

Mr Downer told ABC Radio in February 1999 that the government could not confirm reports the Indonesian military was arming militias in Timor Leste.

"The Indonesian military are denying this," he said. "It's obviously very hard for us to verify one way or the other."

At a press conference later that month he said he had assurances from Indonesia's then foreign minister Ali Alatas that Indonesia was not supporting the militia.

"He explained to me that they weren't giving arms out to pro-integrationists. But what they were doing was what they were doing in all the provinces.

"And that is that they do have some civilian people who help in a policing function."

Mr Downer made similar comments a few weeks later after a massacre at Liquica, in which scores of people were killed.

Howard government's policy 'was to keep Timor in Indonesia'

Professor Clinton Fernandes at the University of NSW was in 1999 the principal intelligence analyst for East Timor at the Australian Theatre Joint Intelligence Centre (ASTJIC) in Sydney. He says Australia's stance at the time had the effect of "providing diplomatic cover to the Indonesian military's activities".

"Howard and Downer went out of their way to absolve the TNI," he said.

"These cables essentially confirm that the Howard government's policy was to keep Timor in Indonesia. And at the end it was forced to backflip," he said.

The Australian cables at the time show Australian intelligence analysts had overwhelming evidence as early as April 1999 — contrary to what Mr Downer was saying — that the Indonesian military was arming the militia units, and that these links went to the top of the army, namely the armed forces chief General Wiranto.

The ABC has sought comment from Mr Howard, but he has yet to respond. Mr Howard was understood to be overseas this week.

Australia's sudden backflip on its support for a peacekeeping force came only after the referendum results were announced — and after another massacre at Suai — when the US stepped in to pressure Indonesia to act.

An unclassified cable from September 9, 1999 from the US embassy in Canberra recounts a 40-minute private meeting between Admiral Dennis Blair — then Commander of American Forces in the Pacific — and Indonesian General Wiranto.

Admiral Blair's two-page talking points urged General Wiranto to "pull back from the brink of disaster; and called for immediate evidence of this".

"Despite repeated assurances that TNI [the Indonesian armed forces] could fulfil its obligations to maintain security in East Timor, despite sending substantial numbers of new troops to the territory and taking the extraordinary step of imposing martial law, East Timor has descended into anarchy," he wrote. "Further deterioration of the situation will not only cause unnecessary loss of life, it will do potentially irrevocable damage to Indonesia's relationship with the rest of the world, including the US. "As you know, a coalition of concerned nations is willing to send a multinational force to East Timor; such a force would aim to stabilize the situation until the MPR [the legislative branch in Indonesia's political system] meets to endorse the outcome of the election, then new arrangements would be made with the UN. "The whole world is watching as this tragedy unfolds, and international condemnation of Indonesia has grown to a fever pitch. The window of opportunity in which Indonesia can salvage its relations with the world is rapidly shutting."

Within days Indonesia allowed an international peacekeeping force into the country, although a declassified document from the Defence Intelligence Agency shows how Indonesia made a last bid to exclude Australia from the force, but failed.

The Australian-led Interfet forces arrived in Timor Leste on September 20 and by the end of the month the militia violence had diminished and Indonesian soldiers began to withdraw.

Professor Fernandes emphasises that it was not Mr Howard but US pressure on Indonesia that resulted in lower casualties.

"The deduction I draw is that the government was prepared to leave the Timorese to their fate," Professor Fernandes said.

"The Interfet mission was the opposite of what Australia had originally wanted."

'The militias must be disarmed'

One declassified cable from the US embassy in Jakarta shows the US maintained a continuing tough stance towards Indonesia as the Interfet mission proceeded.

The then US defence secretary William Cohen met General Wiranto on September 30, 1999 and made clear that the US relationship with Indonesia was on the line unless it stopped the rampage of violence.

An Indonesian soldier kicks an East Timorese student to drive him from the grounds of the Foreign Ministry in Jakarta, June 12, 1998. ( Reuters )

"TNI support for the militias was overwhelmingly apparent and totally unacceptable," he said.

"The militias must be disarmed. The refugees in West Timor must be allowed to return home in safety. Interfet must be allowed to do its work without being harassed.

"There had to be a transparent accountability to deal with those who had committed atrocities. Without these steps, we would be unable to consider a restoration of a normal relationship."

Other US cables show that Australia was unprepared to support a peacekeeping mission, even as the first Interfet troops went into Timor Leste in September 1999.

Australia had to scramble to supply all the necessary logistical equipment because it had lacked any advanced plan for preparing a peacekeeping force.

One unclassified document from the US Pacific Command shows that even as the Interfet force was deployed, Australia was still trying to source 4,000 flak jackets, and had to borrow from the US.

"Australia has chartered commercial transportation to move body armor from DLA Depot, Columbus Ohio to Chicago Airport, for transportation to Melbourne ETA Darwin on Saturday," the cable reads.

"Project to arrive in time to meet Australian deployment planning needs."

Similar time constraints meant there was a shortage of fresh food and strict water rations as the first Interfet troops arrived in the country.

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