Yogyakarta – East Timor's Foreign Minister Jose Ramos-Horta said on Saturday he doubted allegations Australian troops tortured pro-Jakarta militiamen and shot one in the head during a peace mission in the territory in 1999.

The Australian military revealed two years ago it was investigating alleged misconduct by its elite Special Air Service (SAS) over an ambush near East Timor's border town of Suai in which two militiamen were killed and others captured.

But the incident was thrust back into the spotlight on Thursday by reports that UN investigators had exhumed the bodies of the two militia members and would investigate allegations one of them was shot or kicked in the head.

"I don't think there was any torture or any deliberate harm done [to the militiamen]," Ramos-Horta told Reuters on the sidelines of a meeting between six Southwest Pacific nations in the Indonesian city of Yogyakarta.

But the former Timorese independence campaigner said he had full confidence in Australia's military to probe the matter. "If the information is well founded, they will take the necessary action within Australia," he added.

The allegations threaten to sully the highly-praised role Australia played in leading a United Nations force in East Timor after a vote for independence from Indonesia sparked violence by pro-Jakarta militia.

The UN, which ran the territory after the vote and until formal independence in May this year, estimates around 1,000 people were killed in the mayhem.

The investigation is examining allegations over the cause of one of the men's deaths on October 6, 1999, and claims some of the prisoners were treated brutally and tortured during interrogation. The UN exhumed the bodies as part of a routine procedure into violent deaths.

East Timor, a former Portuguese colony, was accepted as the 191st member of the UN late last month. Although the UN has transferred its local powers to the new government, its peacekeepers are still active there.