Mr Downer has reaffirmed that the Indonesian ambassador (mr) Hamzah Thayeb will soon return to Canberra.
Indonesia recalled the ambassador in response to Australia's decision in March to grant visas to 42 asylum seekers from the troubled Papua province.
Mr Downer has told the ABC he is confident the conflict between the two countries will soon be resolved.
“I think ultimately there will be a meeting between President Yudhoyono and the prime minister, and I think that will be symbolically a very important meeting. I'm sure it will be a very important meeting in substance as well, but it will also be symbolically very important.”