http://www.abc.net.au/rn/talks/bbing/stories/s1121412.htm

[This] would allow time to convince the East Timorese of the benefits of autonomy within the Indonesian republic.

December 1998

http://www.abc.net.au/rn/talks/bbing/stories/s1121412.htm

Australian intelligence agencies reported that the Indonesian military was coordinating violence against East Timorese independence supporters from the very beginning. The Australian Department of Intelligence reported as early as January 1999 that militia violence in East Timor was controlled by the Indonesian military.

The Sydney Morning Herald attained leaked Australian classified intelligence of Indonesian military intercepts from February 1999.

Sydney Morning Herald March 14, 2002 Australia's bloody East Timor secret Spy intercepts confirm Government knew of Jakarta's hand in massacres By Hamish McDonald, International Editor

Contrary to John Howard’s claims, the Australian government argued against peacekeeping forces, despite full knowledge of Indonesian military black operations.

The Bulletin magazine attained confidential cables, exposing that the government had argued against peacekeeping forces as early as February 1999.

Australian defense intelligence reported in March that the Indonesian military was coordinating militia violence in East Timor. The intelligence reports were cited in the Australian Senate. Mr Kevin—Yes. Most of them appeared in the Bulletin article on 12 October headed, ‘The Timor cables: what the government knew, what we did not’, but many of them had already previously been reported. Mr Brereton, for example, was quoting from them in the parliamentary debate on 21 September. But there was a Defense Intelligence Organization report as early as 4 March that said: A DIO classified intelligence brief to Ministers reported that The Indonesian Military were arming and organising militia intimidation.

Days later the Howard cabinet continued to conceal the fact that the Indonesian military was responsible for orchestrating militia violence.  7 March 1999: Downer Interview with Laurie Oakes on the Sunday Program. it certainly isn’t something that’s been condoned by General Wiranto, the head of the armed forces. But there may be some rogue elements within the armed forces who are providing arms

Not only did intelligence briefs inform ministers that the Indonesian military was arming the militia, the Indonesian government actually admitted as much to the Australian foreign minister, Alexander Downer.

The leaked confidential cables revealed conversations between Alexander Downer and the Indonesian foreign minister, Ali Alatas.

MEETING 23rd FEBRUARY 1999 JOHN LYONS:

At that meeting Alexander Downer raised the issue of the military, the TNI, providing arms to militia groups. He said, "This is the legitimate arming of auxiliaries," so the Indonesian Foreign Minister was saying the arming of the militia was legitimate.

7 march 1999

ALEXANDER DOWNER, FOREIGN MINISTER: The Indonesian Government, when we've raised it with them, including when I raised it with Ali Alatas the other day, have said that it certainly wasn't happening, that they weren't arming paramilitaries.

On the 6th April, the military and militia set fire to local villages and 100’s of civilians were forced to seek shelter in Liquica church.

The refugees were then systematically massacred inside the church by the militia and military squads, hacked to death by machetes or executed by firearm. The victims were then loaded on to trucks and disposed of.

On the 12th of April the Military abducted six people, including primary school teachers, who were suspected of being pro-independence sympathizers.

The six were taken to Kailako Military Rayon Command where they were detained, interrogated and tortured.

The next day at around 0600 am, they were taken and executed in front of mourners from previous murders. According to witnesses' statements military leaders threatened the mourners announcing that anyone who opposed the Army or the government of Indonesia would meet the same fate.

Witnesses

Mr Downer, in his press conference on 4 September, told journalists:

We have played an enormous role in making what has happened over the last few weeks possible, an enormous role ... I think we have calibrated this pretty much right all along. In that instance, ‘we’ is Australia.

In one city, Maliana, Dili, peacekeeping forces encouraged men women and children to seek refuge in the police barracks where they would be later slaughtered by the military and the militia. The victims were then taken away in pickup trucks.

The Australian government claimed that they had no information forecasting post ballot violence; however the office of national assessments was reporting that all Australian intelligence agencies were predicting the potential for large scale violence after the ballot.

Intelligence officer, Captain Andrew Plunkett, spoke out about the government’s prior knowledge.

After the Government failed to inform peacekeepers of expected violence, Australian defense personnel were ordered to cover up the massacres. While the official death toll from the Maliana police barracks massacre is 47, Captain Andrew Plunkett estimates it was closer to 200.

Leaked Defense intelligence documents echoed Plunketts concerns.

Howard’s cabinet was furious over leaked intelligence, which exposed their lies, their prior knowledge of military involvement, their policy of opposing peacekeepers, and finally their participation in covering up post ballot massacres. The Federal Police launched a dragnet investigation covering a range of Defence Force personnel, government officials and media outlets.

SBS REPORTER: So is Australia holding information today that could lead to the conviction of Indonesian Army figures.

CAPTAIN ANDREW PLUNKETT: Definitely.

SEE NO EVIL: DATELINE

General Wiranto, Commander of the Indonesian Military, who was directly linked to the militia in leaked Australian Intelligence documents, escaped trial. By April 19, both ASIS and DSD have directly linked Wiranto with the militia.

A few years after the atrocities, Howard’s cabinet resumed operations with Indonesian Special Forces, in the name of fighting terror.