Waimori – Pro-independence guerillas said yesterday they had seized control of most of the eastern part of East Timor after clashes with retreating militia and Indonesian soldiers.

The commander of the Falintil resistance on the ground in East Timor, Taur Matan Ruak, said his fighters had taken control of areas abandoned by the Indonesian military which had yet to be occupied by international peacekeepers.

Speaking from his mountain headquarters, Commander Ruak said guerillas were still fighting militia and soldiers for control of an area around the southern coastal town of Betano.

Commander Ruak made it clear the guerillas were unlikely to disarm. "We have learned over 24 years that we can never trust the Indonesian military," he said. A decision to disarm is seen as extremely unlikely before Xanana Gusmao, the leader of the guerillas and likely leader of an independent East Timor, returns.

Mr Gusmao, who has called for reconciliation with Indonesia, is seen as the only man with the authority to prevent the guerillas going on a killing spree to avenge the orgy of militia-led violence that followed the territory's August 30 vote for independence. "Xanana should be here as soon as possible – we need him," Falintil officer Falur Rate Laek said.

Falintil set up its semi-permanent base in a river valley in the Waimori region, southeast of Dili, just before the UN-organised ballot.

More than 3,000 refugees are also sheltering there, forced into the mountains by militia violence. A further 10,000 huddle in the surrounding hills.

The guerillas remained in their mountain camps in the weeks leading up to and after the independence vote. Now they are cautiously moving back into towns and villages left devastated by departing Indonesian soldiers.

"There's very few of us and it's a very large area but we've sent people to where TNI [Indonesian army] have left to make sure the population is secure," Commander Ruak said. Western towns such as Maliana, Bobonaro and Suai remain in the hands of militia.