Darwin – The last of Australia's troops are preparing to leave East Timor as the peacekeeping operation winds down.

Australia's national commander in East Timor Lieutenant Colonel Brian Cox said 70 Australian army, navy and air force troops left Dili earlier this week.

A further 45 would return home to Australia in coming weeks.

The return follows the end of the United Nation's three year peacekeeping mission last month, set up to stabilise the nation amid its bloody push for independence.

A new smaller UN political mission has been established to help build the impoverished new nation.

The UN arrived in East Timor in September 1999 after locals voted overwhelmingly for independence, sparking attacks from pro-Indonesia militia.

About 5,000 Australian peacekeepers were among the 11,000 UN troops at the height of the mission.

"I feel we have actually completed the mission quite successfully," Colonel Cox said. "We are very proud of what the Australian Defence Force has achieved over here, and we are also immensely proud of what the East Timorese are achieving.

"The place we came to in 1999 was in turmoil. As we leave there are prospects for great economic growth and prosperity."

The last Australian flag would be lowered at the base at a ceremony on June 13, he said. Two Australian majors would remain behind until July as the UN establishes its new mission, which will include 15 military training advisers.