Indonesia's President Susilo Bambang Yudhoyono says Australia respects and supports Indonesia's sovereignty and sees Papua as part of Indonesia.
Speaking at the end of a visit to Darwin, he said Papua was legitimately part of Indonesia, and Jakarta is doing everything it can to create welfare and justice there.
Under the 2006 Lombok Treaty, neither government will intervene in the internal affairs of the other.
Indonesian reports say the president also discussed the possibility of having Australia donate four Hercules C-130 planes to help with natural disaster management.
Australian civil society groups staged a rally outside the building where the leaders met, demanding that Canberra pressure Indonesia to prosecute those behind recent deadly shootings in Papua and end a ban on international media reporting from the region.