Dennis Schulz and Louise Williams – Pro-Indonesian militias are fleeing East Timor ahead of the arrival of peacekeepers, some saying they fear they will now be killed by Indonesian troops to wipe out evidence of Jakarta's leading role in the carnage.

Refugees in Darwin and church sources working in West Timor, where about 130,000 refugees have been forced into militia-controlled camps, reported new fears that Indonesian troops would kill militia members themselves, after using the thugs to kill independence supporters, priests, nuns and civilians.

"The Indonesian Army wants to exterminate the militia because they want to take away all trace," said a refugee from Dili, Mr Alberto Fernandes Belo, who is now in Darwin.

"The militia know about the Indonesians' plans to kill and burn [following the victory for independence supporters in the United Nations vote]. That's why they want to finish the militia."

Mr Belo was one of thousands who had fled to Dare in the hills outside Dili, before returning to join evacuees who arrived in Darwin yesterday. He said militia members now feared for their lives and sought shelter from the refugees.

"The people accept the militia," he said. "If they come with guns, they disarm them. Then they console them. They will face justice in the future."

The reports were backed up by a UN official still in Dili who said the militia appeared to be preparing to pull out of Dili. "There are still some militia people on the streets with weapons, but generally they seem to be preparing to move out," said Mr Colin Stewart, one of 12 UN staff remaining after Tuesday's evacuation of the UN headquarters in the city.

From West Timor, church sources reported militias crossing the border had spoken of fears of being exterminated as Indonesia came under increasing international pressure over human rights abuses in East Timor. However, others said the militia would continue to be used as a frontline force to "take the bullets" in any engagements with peacekeepers.

"We know that an increasing number of militias are crossing over from East Timor into West Timor ahead of the peacekeeping force and now there are anywhere between 8,000 to 14,000 armed militias in West Timor," said the source.

The militia gangs are virtually in control of the provincial capital, Kupang, where locals say they have taken over restaurants, demanding free food, and forcing shop owners and even petrol stations to hand over goods and petrol free. With the clear failure of the Indonesian military's plan to use the militias to intimidate the East Timorese into voting against independence, Jakarta faces a serious problem over what to do with the thugs.

According to one Kupang resident, resentment was rising to the point that local youths may be used to kill off the militias in West Timor.

In Darwin, the refugees told how Indonesian troops used the militias to force the mass relocation of thousands of East Timorese to Atambua in West Timor, then told the militias they must also leave or die.

"The militia are finished now in East Timor. Only the army are left. The army will kill the militia," said Mr Carlos Mendoza, 19, of Dili.