The Senate has rejected a proposal for an international war crimes tribunal covering the Indonesian occupation of East Timor. Instead, it backed Indonesian President Megawati Sukarnoputri's moves to prosecute those committing atrocities during the 1999 independence ballot.

Greens Senator Bob Brown said Australia should pressure the United Nations to set up a war crimes tribunal to deal with atrocities in East Timor between 1975 and 1999.

Senator Brown said 2,000 East Timorese were killed during the referendum period but 200,000 were killed during the entire Indonesian occupation, so Indonesia was only investigating one per cent of crimes. But Labor's Peter Cook won government support to change the motion to back Indonesian prosecutions and to note the UN Security Council's lack of support for an international tribunal.

"On the other hand, we do know that the new president of Indonesia, Megawati Sukarnoputri, has set up a new process which will broaden the scope of the special Indonesian court's work in investigating human rights violations in East Timor in the lead-up to the 1999 referendum," Senator Cook said.

"If this matter can be settled with justice and honour within Indonesia that is a far, far, far better outcome than an international body seeking to impose a standard on that country. We call on the Indonesian president and her government to make sure that all necessary steps are taken to bring to justice those responsible for crimes and human rights violation."

Australian Democrats foreign affairs spokeswoman Vicki Bourne said people committing atrocities before 1999 would never be brought to justice without a tribunal. "People know who the individual was who chopped off somebody's head and stuck it on a pole outside a school ... but we will never hear [that evidence] because that tribunal will never happen," she said.

Senator Brown said the Senate lacked in nerve and morality. "I don't accept this amendment because it is simply saying, well, this matter should be left to Jakarta and it should be circumscribed to the events surrounding the referendum in East Timor," he said. "Is the massive rape, death and destruction campaign in East Timor different from that in Rwanda or in Bosnia?"