Indonesia's foreign minster has warned the Government's asylum seeker policies risk jeopardising trust and co-operation between the two countries.
Marty Natalagawa met Foreign Affairs Minister Julie Bishop in New York this week and the two spoke at length about a range of issues.
A statement now released by Dr Natalagawa's department details the discussion, revealing Australia intends to push ahead with turning boats back to Indonesia.
Indonesia has repeatedly warned against the policy, which is part of Operation Sovereign Borders, the Coalition's regional action plan against people smuggling.
The press release from Dr Natalagawa's ministry says that unilateral measures taken by Australia would potentially risk the close cooperation and trust between the countries.
It says he reminded Ms Bishop that the issue of asylum seekers should be dealt with through existing regional co-operation arrangements.
The statement also says Australia wants to work "behind the scenes" and "quietly" on the issue to prevent too much publicity.
Ms Bishop has previously said regardless of how Indonesia views them
Meanwhile Immigration Minister Scott Morrison has arrived in Papua New Guinea's capital Port Moresby ahead of a visit to the processing centre for asylum seekers on Manus Island.
Mr Morrison has visited Papua New Guinea several times, but this is his first trip as Immigration Minister.
His first meeting was with attorney-general Kerenga Kua.
Mr Morrison told Mr Kua that Prime Minister Tony Abbot is grateful for PNG's help in tackling people smuggling.
But Mr Morrison said the agreement with the Rudd government to send asylum seekers to Manus Island needed to be developed further.
"The previous government had put some measures in place. I think we have many challenges ahead to ensure we can get those arrangements on a stable footing," he said.
Mr Morrison will head to Manus Island tomorrow to inspect the processing centre and efforts to increase its capacity.