[New evidence has emerged that the Indonesian army was directly involved in the ambush that killed two Americans and an Indonesian near the Freeport Gold mine in the Indonesian province of Papua last August. Suspicion for the attack initially fell on the Free Papua Movement. But now the Washington Post has reported that Australian intelligence gave its signals intercept to the United States following the attack. The Indonesian military has denied the claim.]

Presenter/Interviewer: Graeme Dobell, Canberra

Speakers: Australian defence analyst Dr Adam Cobb; Australia's opposition spokesman on Foreign Affairs, Kevin Rudd

Dobell: The Washington Post says the US Government believes the top ranks of the Indonesian military aimed to discredit the sepratist Free Papua Movement, and have it declared a terrorist organisation.

The paper says that human intelligence about conversations among Indonesian generals discussing an attack on the mine has been supported by signals intelligence. Those Australian intercepts of Indonesian conversations were passed to the US after the ambush that killed three teachers, two of the Americans. Defence analyst Dr Adam Cobb says Australia has the signals capacity to gather such intelligence about Papua.

Cobb: Well it's very credible. As we saw during the Timor crisis, there was very specific information right down to ... well, from the strategic level between military commanders, the general and major general rank, right down to specific units moving on the ground. I don't think we've lost that capability since Timor, so it's highly likely that's going on.

Dobell: The problem for Australia is that it wants to step up intelligence cooperation with Indonesia to combat terrorism. According to the Opposition spokesman on Foreign Affairs, Kevin Rudd, who is visiting Jakarta, a lack of trust means the intelligence flow with Indonesia has dried up.

Rudd: Problems don't just occur overnight. They occur as a consequence of long-term relationships and I've got to say in this case, the long-term deterioration of a relationship. The immediate challenge on the Prime Minister's part, is to make two things happen. The first is to get back under control and in order the flow of bilateral intelligence information between Australia and Indonesia. Four or five years ago, what former intelligence officers have told me is that there was a large flow of information and that has now dried up to a trickle. That's not me speaking, that's people in the trade. But secondly, it also comes down to practical levels of cooperation now between Australia ... for example the Australian federal police and the Indonesian national police.

Dobell: Australia's Defence Signals Directorate is the jewel in the intelligence crown, the service that evesdrops on phone calls, radio transmissions and data flowing across Asia, especially Indonesia. But is DSD's product so valuable Australia won't use the evidence gathered to confront criminal acts.

The Sydney Morning Herald in March said DSD had explosive evidence of how senior Indonesian generals organised the violence which swept East Timor in 1999. It said the raw Timor intercepts were not given to war crimes investigators for fear of harming intelligence gathering. Dr Adam Cobb says the Indonesian military used violence and militia forces in East Timor and the pattern is being repeated in Papua.

Cobb: Leaked DSD transcripts have shown that there was complicity right up the chain of command, linking the various military commanders right throughout the chain of command, basically, to the arming and the formation of militia in East Timor. We now have evidence, or emerging evidence, that similar activities are taking place in Papua. So there's some very important questions being raise.

Dobell: If the United States wants to use Australian signals intelligence to prosecute, to bring people to justice, what problems does that present for Australia?

Cobb: On the one hand you've got the very important human rights concerns, and you want to be able to prosecute. But on the other hand, from the military intelligence perspective, you don't want to lose this access to this information and these sources. So you've got to be working pretty hard to protect your sources so this information continues to flow in. So it's a very fine balance between using the information and also protecting it.