Australia is restated its support for Indonesia's territorial integrity, saying it wants Papua to remain part of Indonesia.
The Australian foreign minister, Alexander Downer, made the comment in Jakarta at a meeting with his Indonesian counterpart, Hassan Wirajuda.
Their meeting comes just weeks after 43 Papuans arrived in Queensland seeking asylum from alleged Indonesian persecution.
Mr Downer rejected an Indonesian request for access to the asylum seekers who are being held on Christmas island.
The two sides agreed at the Jakarta talks to have joint navy patrols to crack down on illegal fishing.
Papuan separatists have been engaged in a low-level guerrilla war to win independence from Indonesia which has ruled the former Dutch colony since the 1960's following a UN-backed vote.