Sian Powell's exclusive report on atrocities against the people of East Timor during the 24 years of Indonesian occupation, published in The Australianyesterday, was grim reading, detailing anything up to 180,000 deaths, mainly from starvation. Drawing on the previously suppressed report of East Timor's Commission for Truth and Reconciliation, Powell reported its conclusion that the Indonesians killed and kidnapped, starved and tortured tens of thousands. Adding credence to its claims, the commission also finds fault with independence fighters, claiming members of the resistance committed crimes as well. But the overwhelming impression in the commission's report is that across the years from the 1975 occupation to the 1999 evacuation, the Indonesian army acted appallingly. For all of Indonesia's arguments that East Timor was just another province, the military treated it as a battle zone, where every civilian seemed suspect.

Nothing in the report will be news to the people of East Timor. Nor is it intended as the last word on crimes committed under the occupation. At its foundation in 2002 the commission was ordered to pass on serious criminal cases to the courts for prosecution. It is hard to imagine how the people of East Timor could accept anything else. The losses of loved ones are still recent, the wounds of occupation still raw. And even if few trials of East Timorese nationals eventuate from the commission's work, its report still serves an important purpose as a record of the long and agonising birth of the nation. But acknowledging and honouring suffering under the occupation does not mean the East Timorese can afford to be prisoners of the past and the attempt of the Dili Government to play down the report is understandable. A bare five years after their ignominious withdrawal, the Indonesians would not dare alienate world opinion by threatening the fledgling state, but East Timor is desperately poor and incapable of defending itself. Dili needs to be on good terms with Jakarta and has nothing to gain, and a great deal to lose, by denouncing Indonesia.

While President Xanana Gusmao is now in New York to present the commission's report to the UN, that it has been kept under wraps for months until now appears to indicate his attitude. Certainly East Timor's ambassador to the UN says his country is unlikely to seek the prosecution of members of the Indonesian military implicated in atrocities. And on their track record to date, the Indonesians are unlikely to pursue their own with any enthusiasm.

The foundations for this pragmatic response were established by the two countries last August with the creation of a joint commission with no power to punish anybody charged with abuses under the occupation.

None of this will be good enough for East Timorese and their Australian supporters who believe all Indonesians, and their allies, who committed crimes during the occupation should be called to account. And critics of the way the Indonesian army deals with rebels will warn it sends a signal that the international community will ignore acts of injustice, even crimes committed by members of its military. Certainly supporters of the West Papuans who landed on Cape York on Wednesday will want Australia to accept them as refugees. And so we should – if they meet the criteria that applies to all asylum-seekers. But there is no case for the Australian Government sticking its bib into Indonesia's business and accepting them as freedom fighters while we accept its long-established sovereignty over West Papua.

It is never wise to jeopardise international relations – especially between neighbours – with single-issue stances. East Timor's determination to get on with Indonesia makes the point. It is often best to acknowledge past wrongs, while leaving them unavenged.