Craig Skehan – Australia and New Zealand will press Indonesia's visiting President Wahid to prosecute members of his country's military, and militiamen, over atrocities in East Timor. But the Prime Minister yesterday also pledged support for Indonesia's "territorial integrity" in the face of secessionist conflicts.

Mr Wahid, who in August faces impeachment, began his trip on an unfortunate note, with an aircraft problem stranding him temporarily in Darwin. And in what could be seen as an irony, the former commander of Australia's forces in East Timor, Lieutenant-General Peter Cosgrove, was among those at Fairbairn RAAF base in Canberra for Mr Wahid's arrival.

Mr Howard told Parliament that his counterpart's much-postponed trip was warmly welcomed as a shift from past bilateral tensions."This is a very important visit." But officials said the Foreign Minister, Mr Downer, would raise with Mr Wahid today his Government's failure to prosecute many military and militia figures involved in the killing of pro-independence East Timorese.

Unless stronger action is taken to overcome military resistance to such prosecutions, Australia is expected to back calls for an international war crimes tribunal.

Asked on his arrival in Canberra last night what his response was to Australia's push for action over the atrocities, Mr Wahid said: "I have to discuss it with the Foreign Minister first." His advisers said there was a need to entrench democracy in Indonesia, and the President's authority, to improve the Government's ability to deal with human rights violations.

New Zealand's Prime Minister, Ms Helen Clark, said that she would ask Mr Wahid, due to visit her country tomorrow, to do more to disarm East Timorese anti-independence militias. The NZ Government is also threatening to support calls for a war crimes tribunal because of the severe limits on prosecutions and the extremely light sentences given to the few people who have been convicted. Some commentators fear that a tribunal would be exploited by political and military foes of Mr Wahid on the ground that it would be a violation of Indonesia's sovereignty.

Mr Howard told Parliament: "Everyone in the House knows that relations between Australia and Indonesia went through a difficult time over matters concerning East Timor." Australia wanted to "move on" to strengthen bilateral relations. Mr Howard said Australia would continue to support Indonesia's territorial integrity and expressed hope that secessionist tensions could be resolved.

The Opposition Leader, Mr Beazley, asked by journalists about the call from the Government back bencher Mr Andrew Thomson for negotiation of a security treaty with Indonesia, said: "Well, it's not on our agenda that we should do that. But that's not to say that you wouldn't be in a position to have discussions about regional security with Indonesia." A security treaty, signed in 1995 by the Labor prime minister Mr Paul Keating and President Soeharto, was abrogated by Indonesia in 1999 amid diplomatic clashes over East Timor.

Mr Downer was asked in an ABC interview yesterday if Australia could have a formal security relationship Indonesia as it became more democratic. "I don't think you need a security treaty in order to do that," he said. "But your point is generally right – I think it's important we do have links with the security apparatus in Indonesia, which we do have."