The Commission of Truth and Friendship will formally submit its findings to Indonesia's President Susilo Bambang Yudhoyono and his East Timorese counterpart, Jose Ramos-Horta later today. The 300-page report was prepared by a Commission set up by both governments, to hear evidence of crimes against humanity committed around East Timor's vote for independence in August 1999. If accepted, it'll be the first time Indonesia acknowledges the role of the military, police and civil government in the violence.

Presenter: Sen Lam

Speaker: Alexander Downer, Australian foreign minister from 1996 to 2007

Lam: Alexander Downer if the government at the time, the Howard government knew of the impending violence why did Australia not do anything to prevent it?

Downer: Well we did an enormous amount to prevent it, how quickly one forgets what happened. First of all you might recall that there was a commitment of UN police, of course many of whom were Australian but not all of whom were Australian, so that was the first thing.

Secondly in April of 1999 the then prime minister and I organised a summit in Bali with President Habibe, General Wiranto who was the defence minister and also Ali Alatas who's the foreign minister, and that was the point of the summit to talk about the violence that was taking place and our concerns that the Indonesian military were involved in that violence.

Lam: But by then hundreds of people had already died at the hands of the Indonesian backed militias. Why was security precautions not put in place before the vote?

Downer: Well when you say why weren't security precautions not put in place before the vote, they were, but of course this was part of Indonesia and so the Indonesians made it perfectly clear from the time they decided that there would be a referendum, which was I would have to double-check that, which was probably about March, they make it perfectly clear that they wouldn't have any foreign involvement in security. And nevertheless they were prepared to allow a UN presence there and the UN to supervise the vote, and they were prepared to allow some UN police there. But that was all.

So the more that we pushed for some kind of a peacekeeping force the more resistant they were to that idea. Of course it wasn't just us, I mean let's not just focus on Australia, importantly the UN shared this view. The UN's people were on the ground so they were particularly concerned about their own people. So we certainly pushed for it, but you need to understand Indonesia. Indonesia was a country that was colonised by Europeans for hundreds of years and gained its independence formally in 1949, and the last thing Indonesia wanted was to have foreign troops on its soil anymore. That's an article of faith for a country like Indonesia.

Lam: Indeed and you said that helping free the people of East Timor was among your greatest achievements as foreign minister. That's been seen as quite triumphalist in certain sections of Indonesian society. Do you regret saying that?

Downer: No of course I don't regret it, I don't care whether they think it's triumphalist or not, it's not a matter of dramatic indifference to me. I know some sections of Indonesian society you know how it is; you're in the media they're always people who criticise you. That's just how I feel, and I'm not the foreign minister anymore and so I'm quite happy to say what I actually feel. Whether people think it's triumphalist or not it's a matter of indifference to me.

Lam: Well returning to this commission's report, do you think there should be a Cambodia-like international tribunal to bring the perpetrators to justice?

Downer: I think to be honest with you that's really not a matter for me or for Australia, I think that's a matter for the East Timorese. I think they've got to work out in their own minds what they think is the best way forward. There are a number of things that they would like no doubt, I know this from talking to them over the years on this topic. There are a number of things that weigh on their minds.

The first is of course justice, justice for those who suffered. But the second thing that's on their mind is that they've got to live for now and forever with Indonesia. So they have to take all those things into account. That's why it's best to leave that decision to them.

Lam: Well the Commission of Truth and Friendship is meant to help both countries move forward.

Downer: Yeah exactly.

Lam: To manage future bilateral ties, but what's the sense of justice there if the perpetrators are not being brought to book as it were. In fact even President Yudhoyono refuses to apologise?

Downer: Well whether they apologise or not is one thing, but another will be whether the people involved are brought to justice or anymore of them will be brought to justice. There have been some trials in relation to what happened in East Timor.

Lam: Yeah but no one's in jail though?

Downer: No, well I'm not sure about that, maybe or maybe not, but you might be right, but that really is a matter between the East Timorese and the Indonesians. I'm not sure whether Australia should be making that a bilateral issue between Australia and Indonesia. I'm not quite sure why for us we would be making such a big issue of that, I would have though it was much more a matter for East Timor. If East Timor wanted to make a big issues of that and of trials and of in particular fingering people who they felt was specifically responsible then they should take that up with the Indonesians and there may be a case for Australia and perhaps even if the UN supporting them in that context. But of course there are real questions about within the Indonesian military who was behind this.

My own view of it, this is contested by some, but on the other hand I had a fair bit of information available to me at the time, is that this was certainly not the policy of President Habibe. Nevertheless I think General Wiranto as the defence minister absolutely knew what was going on. I mean he couldn't have failed to have known what was going on. I'm not sure whether he particularly supported it, but he simply didn't have the strength to stop it.