An international relations academic says Australian peackeeping troops are being withdrawn from East Timor prematurely.

The Australian Defence Force will hand over control of its base in East Timor to the country's government during a ceremony today. The ceremony will mark the end of Australia's peacekeeping operations in the country. A small number of troops will remain as part of a defence cooperation program between Australia and East Timor.

Senior lecturer in international relations and strategy at the Australian National University, Michael McKinley, says there are ongoing security concerns in East Timor, due to the traumatic nature of its transition to independence.

"Although there's going to be a defence presence left in the country ... the peacekeeping presence could perhaps have been extended, particularly if there are any reservations whatsoever in the East Timorese Government about their ongoing security concerns," he said. "My understanding is that there are certainly some concerns still remaining."

Dr McKinley says the Australian troops could have stayed for another year. "For the sort of psychological security of the East Timorese and perhaps even as a general message to the residue of trouble making, I thought perhaps Australia might have stayed somewhat longer," he said.

The commander of the Australian forces in East Timor, Lieutenant Colonel Brian Cox, says he believes the country is being left in safe hands. "We came in here in a period of turmoil in 1999 with INTAFET and General (Peter) Cosgrove leading the 5,000 Australians then, and we're now leaving with economic prosperity now in place," he said.