The Australian Federal Police announcement that it will investigate charges of war crimes against perpetrators of the murder of five Australian based journalists in the East Timorese town of Balibo in 1975, has put a legal cat among the diplomatic pigeons.

Already senior Indonesian politicians have objected, saying they will not cooperate with such an investigation, while the Australian government and department of Foreign Affairs and Trade is going into a now well practiced mode of damage control.

The Australian government, including PM Rudd and Foreign Minister Smith, have predictably — and correctly — said that the matter is a judicial one that does not involve political intervention. Indonesia’s President Yudhoyono is likely to say much the same, although a government spokesman has already reacted with some hostility.

The questions now are whether AFP members will need to travel to Indonesia to collect evidence and be allowed to do so, whether charges will ultimately be laid, and whether Indonesian courts will uphold the provisions of an extradition treaty to allow those who may be charged to be tried in Australia.

One objection to the investigation, from Indonesia as well as from some pundits in Australia, is that the crime was committed too long ago and should not now be allowed to disrupt otherwise good bilateral relations. Some also note that the Indonesia of 2009 is a much improved place over that of 1975.

Indonesia is indeed democratising, and paying much greater respect to the rule of law. It is also true that Indonesia’s statute of limitations for conventional criminal charges has been exceeded. However, under international war crimes provisions, there is no statute of limitations; witness the pursuit of war criminals decades after the end of World War II, and from Pol Pot’s Cambodia.

Further, for Indonesia’s democracy to be more than procedural, impunity from rule of law must cease. Indonesia has a long history of unresolved gross human rights violations, and cooperating with the AFP investigation would be one important step in ending that culture of impunity.

However, many in Indonesia remain untrusting of Australia’s intentions, do not accept the separation of powers between government and judicial processes, and are in many cases still mired in authoritarian thinking.

The reality is that if charges are finally laid — and this is by no means a certainty — then extradition from Indonesia will still face a large and probably insurmountable hurdle.

In the meantime, the roller-coaster that is the Australia-Indonesia bilateral relationship is again plummeting, and its much-touted “maturity”, and that of the respective political leaders, will be tested on the way down.

Associate Professor Damien Kingsbury is from the School of International and Political Studies at Deakin University, and is a member of the Balibo House Trust.