Rachael Brown reporting

Emma Alberici: A leaked report into the handling of East Timor's 1999 independence referendum is being celebrated as a crucial step on the road to reconciliation.

The ABC has obtained a copy of the report to be released in a special ceremony by the presidents of both nations next week.

The bilateral body, the Truth and Friendship Commission has spent more than two years investigating the events and concludes that the Indonesian military, police and government must all share the blame for gross human rights violations carried out by militias and targeted against East Timorese independence supporters

Australia played a leading role in East Timor and now Alexander Downer, Australia's former foreign minister has found himself defending the Howard government's handling of the situation, as Rachael Brown reports.

Rachael Brown: As violence gripped the streets of Dili in 1999, many working on the ground doubted the militia was behind it.

James Dunn: But actually by Indonesian troops using militia cloaks to look as if they were militia. There's no doubt about that and of course there was no doubt about those earlier atrocities. The one at Liquica earlier, and then of course later at Suai, Maliana, were actually conducted by Indonesian military officers.

Rachael Brown: James Dunn was one of them, appointed a UN expert on crimes against humanity and stationed in Dili during the independence vote, he witnessed the violence first hand.

He's stunned by the findings of the bilateral Truth and Friendship Commission. The report which is yet to be released publicly, details murder, rape, torture, illegal detention and forced mass deportations.

James Dunn: What is very strong about it, is that Indonesia has virtually agreed, consented to the release of a report which points to the responsibility of the Indonesian military.

But, you know, its shortcoming of course it that it only deals with events of 1999 and that was merely the tip of the iceberg.

The biggest atrocities took place during earlier periods of the Indonesian occupation. One of the them when over 1,000 people were killed in a couple of days as a reprisal. These aren't really taken up in that report.

Rachael Brown: And it also doesn't name any names or recommend specific prosecutions so can it be argued, it's really not that beneficial?

James Dunn: Well, I think it is beneficial in one way. That the presence of the powerful military as it stands, largely unreformed, is still a major obstacle to the fulfilment of democracy, and they would like it brought out and there is this new mood about it.

I think many Indonesians would like to see this brought out. It's the kind of report which really, we can't turn away from.

All the parties involved must now face the reality that the issue has to be taken seriously and it does now require a much more serious legal action.

Perhaps that international tribunal that the Indonesians didn't want and nor did the Howard government and other, some other Western governments. They were opposed to it.

Rachael Brown: How do we go about getting an international tribunal?

James Dunn: Well, I think one way of doing it would be to raise the issue with the Indonesians and encourage them to move in that direction. It really means exposing those elements, really the hangover the Suharto regime whose presence in senior posts or in politics really is an embarrassment to Indonesia.

And I think really, for Indonesia it's the best way to go. Indeed, it would be tragic if they didn't face it.

Rachael Brown: Australia responded to the violence in East Timor by sending in a peacekeeping force. But that doesn't let Australia off the hook, says retired diplomat, Bruce Haigh. He served in Indonesia in the '80s and says Australia knew who was behind the atrocities, but chose to sit on the information.

Bruce Haigh: Why did they sit this information? Why didn't they make it public? To what end were they withholding this information? Why is it that Australia has consistently, when under pressure, sought to protect the evilness that exists from time to time at the hands of the Indonesian police?

Rachael Brown: The former foreign minister, Alexander Downer, who's soon to take up a peacekeeper posting with the UN, has fired back.

Alexander Downer: But I mean, what were we supposed to do? I often say this; what were we supposed to do? Were we supposed to send the SAS into Indonesia, into East Timor which was then part of Indonesia?

Should we have declared war on Indonesia over East Timor, and I think the answer to that is no and I think Australia, by the way did a magnificent job through all the difficulties and they were manifold difficulties on the East Timor issue through 1999 and into 2000.

Rachael Brown: Mr Downer says he's always believed elements of the Indonesian military and perhaps officials were behind the East Timor atrocities, but he says he doesn't know the extent to which the then Indonesian military commander, General Wiranto, sanctioned any of it.

Alexander Downer: My guess is he knew what was going on, and contrary to a popular belief that he was a big strong man, he didn't really have the strength within the Indonesian military to close it down. I don't think he was particularly in favour of it, but he didn't have the strength to stop it happening.

Emma Alberici: That's former foreign affairs minister, Alexander Downer.