Foreign Minister Stephen Smith told parliament families may have to wait for some time for the remains to be returned, The Australian reported.
"This process always takes much more time than the families would want and we understand that," Smith said.
The crash in difficult terrain near Kokoda killed all 13 people on the Twin Otter plane. Eight were Australian trekkers planning to hike the Kokoda Trail, while the others were an Australian guide for No Roads Expeditions of Melbourne, two Papuan porters and the crew of the plane, The Australian said.
Joseph Kintau, director of civil aviation in Papua New Guinea, reported three bodies had been recovered.
Airlines PNG said the pilot, Jannie Moala, 26, had been certified to command a passenger aircraft for only six months. But the airline described her as an experienced pilot who was familiar with the area around Kokoda and had 2,500 hours of experience in the model of Twin Otter involved in the crash.