Dan Box, John Kerin – East Timor Prime Minister Mari Alkatiri has declared that the fledgling nation does not need Australia's help to deal with border skirmishes.

Dr Alkatiri, who is in Australia to sign a resources deal, was responding yesterday to an incident in which East Timorese police shot and killed three Indonesians and former militia members.

East Timor claims the three men, former members of the Red and White Iron militia who moved to East Nusa Tengarra after East Timor's violent separation from Indonesia in 1999, entered the country illegally and attacked police.

But Indonesia Foreign Minister Hassan Wirayuda condemned the shooting, saying the East Timorese used excessive force.

Indonesian military officials have alleged the three men intended to fish in a nearby river when they were shot last week.

Dr Wirayuda has demanded the two countries establish a joint investigation.

East Timor's police chief, inspector Ismail Babo, handed over the bodies of Candido Mali, 24, and Stanislao Maubere, 40, to Indonesian police yesterday. The other dead man was Jose Maria Freitas, 38. The killings sparked protests in West Timor town of Atambua involving about 1500 former militiamen, who burned posters of East Timor president Xanana Gusmao.

Dr Alkatiri said Australia had helped train the East Timorese police and military to the point where it could deal with the situation.

"We have good relations with the Government in Jakarta and we do believe that through diplomatic channels we will reach agreement on this," he said.

Australia deployed more than 4000 troops to East Timor during its battle for independence in 1999 but has wound down its presence to fewer than 50 troops.