Relations with Indonesia are facing new tests amid claims Australia spied on the Yudhoyono Government over a trade dispute it had with the US.
As Immigration Minister Scott Morrison rejected Indonesian navy claims that Australian ships deliberately entered Indonesian waters, documents released by fugitive US security contractor Edward Snowden suggested Australia offered the US information from its eavesdropping activities.
The Snowden documents, seen by the New York Times, showed the Australian Signals Directorate offered to share with the US National Security Agency details of talks between an American law firm and Indonesian authorities.
The law firm was helping Indonesia in a dispute over clove cigarettes.
The documents' release comes after revelations Australia had tapped the mobile phones of President Susilo Bambang Yudhoyono and his inner circle, including his wife. Indonesia downgraded its relationship with Australia in response to those revelations.
Prime Minister Tony Abbott refused to be drawn on the documents but said Australia did not gather intelligence to the "detriment of other countries".
"We use it to uphold our values," Mr Abbott said. "We use it to protect our citizens."
The Indonesian Government called in Australian Ambassador Greg Moriarty last week to complain about Australia's use of lifeboats to send asylum seekers back into Indonesian waters.
An Indonesian navy report leaked at the weekend said Australian warships had entered Indonesian waters often and with ease and suggested it was done deliberately, saying with current navigational equipment an accident seemed unlikely.
Mr Morrison told ABC TV an unclassified report into the incident would be made public.
He said "it wasn't intentional at all" for Australian ships to end up where they did.
A Senate order requires Mr Morrison to release the full report by today.