Dennis Shanahan and Stephen Fitzpatrick – Kevin Rudd has been forced to make plans with Indonesia's President Susilo Bambang Yudhoyono to avoid any diplomatic rupture caused by the Australian Federal Police's inquiry into possible war crimes in East Timor.
The Australian government was caught with little time to cushion the impact on Australian-Indonesian relations of the investigation, announced by new AFP Commissioner Tony Negus only days after his appointment.
The Prime Minister spoke to the Indonesian President by phone on Sunday and the two leaders agreed to co-operate to ensure disruption in the sometimes turbulent Australian-Indonesian relationship was minimised.
A spokesman for Mr Rudd said the two "agreed to find ways to manage this question in a way that least affected the bilateral relationship".
But there has been criticism of the AFP's decision in Jakarta and last night Indonesia's military said it would refuse to co-operate with Australian police in any inquiry into the killings of five Australian-based journalists in Balibo in East Timor in October 1975.
In 2007, a NSW coroner ruled that the killings of the so-called Balibo Five were likely to have been a breach of the Geneva Conventions, and referred the matter for further investigation. Last week, soon after being sworn in, Mr Negus announced a criminal investigation into allegations of war crimes, following testimony at the inquest into the death of one of the five, Brian Peters, that Indonesian military officers ordered their killing during an invasion of East Timor.
Foreign Minister Stephen Smith contacted Jakarta before the public announcement but Mr Rudd spoke to Dr Yudhoyono on Sunday.
Last night Indonesian Air Vice Marshal Sagom Tamboen said there had been no formal request for assistance from the AFP, "and hopefully there will be none, because for us the problems of Indonesia and East Timor are in the past".
"This was the decision of the Indonesian and East Timorese governments when they accepted the Truth and Friendship Commission report, that it was done with," he said.
That report, handed down in July last year, found that Indonesia bore "institutional responsibility" for the violence in 1999, immediately after East Timor's independence referendum.
However, it also allowed Jakarta and Dili to resolve not to launch prosecutions on the basis of any evidence given to the commission, which prompted the UN to withhold its support from the five-year inquiry.
Air Vice Marshal Tamboen said the Balibo inquiry was purely a domestic affair for Australia. "If they want to investigate this, they must do it as an internal matter," he said. "What help is there remaining for us to give? We've done with it."
One of the two men named in the report of NSW Deputy Coroner Dorelle Pinch last year was retired army captain Yunus Yosfiah, who rose to become information minister in the post-Suharto years. Both he and the other man named, Christoforous da Silva, were members of Indonesia's special forces in 1975.
Foreign Ministry spokesman Teuku Faizasyah said yesterday that, while the granting of visas for any AFP officers to conduct inquiries in Indonesia would be a question for the immigration department, he would be "surprised" if it occurred.