Protesters in East Timor have staged a demonstration against Prime Minister John Howard as he left Dili, accusing Australia of interfering in East Timor's political affairs.

Mr Howard flew to East Timor this morning to meet Australian troops in Dili and hold talks with political leaders, including President Jose Ramos Horta, regarding the country's security and Australia's troop presence.

Mr Howard also had lunch with several hundred soldiers at one of three Australian defence bases.

The visit coincided with renewed uncertainty over East Timor's future, with still no clear winner from last month's parliamentary elections.

Dr Ramos Horta asked Australia to keep troops in the country until the end of next year to help strengthen the country's fragile security and stability. Mr Howard made no promises, but says Australia will not turn its back on East Timor.

"It cannot be assumed that we will stay indefinitely," he said. "That's not the purpose of our involvement. The purpose of our involvement is to stabilise the situation. "When it's fully stabilised and we are satisfied that it will remain stable is the time to contemplate withdrawal."

Fretilin party protesters this afternoon waved anti-Australian banners.

But before he left, Mr Howard denied Australia was interfering in East Timor's politics.

"We respect the sovereignty of East Timor," he said. "We do not intend to abuse in any way our position by taking it upon ourselves to give public advice to the leadership of this country as to how to handle the democratic process."

The Prime Minister also met United Nations' leaders in Dili, and the interim foreign minister.