Indonesia's foreign minister has divulged the contents of his private discussions with his Australian counterpart Julie Bishop, warning the Government's asylum seeker policies could damage relations.

Marty Natalegawa met the new Foreign Affairs Minister in New York this week and the two spoke at length about a range of issues.

In an unusual step, Dr Natalegawa's department has issued a press release revealing details of the discussion, which included Australia's plan to turn 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 statement says unilateral measures taken by Australia would potentially risk the close cooperation and trust between the countries.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Listen Duration: 3 minutes 33 seconds 3 m 33 s Correspondent George Roberts discusses the statement Download 1.6 MB

It says Dr Natalegawa reminded Ms Bishop that the issue of asylum seekers should be dealt with through existing regional cooperation arrangements.

It also also says Australia wants to work "behind the scenes" and "quietly" on the issue to prevent too much publicity.

The ABC's Indonesia correspondent George Roberts has told PM the statement is a rare move from a nation that is usually much more circumspect in diplomacy.

"Even in recent history, the foreign minister has been very reluctant to speak openly and has been very diplomatic about it," he said.

"So this kind of language is quite strong and quite interesting indeed.

"The foreign minister actually states in this press release that Australia and Indonesia need to take stock in order to identify common interests and that both countries need to basically take a joint approach to this, so it's almost like going back to square one and starting again."

Prime Minister Tony Abbott is due to visit Jakarta next week.

Indonesia should stop pious rhetoric: Downer

Former foreign minister Alexander Downer says Dr Natalegawa should not be "taking shots" at Australia as soon as a new government is elected.

Diplomatic row brewing Alexander Downer's rejection of Marty Natalagawa's comments is significant because he was a minister in the former Coalition government, writes Asia editor Catherine McGrath.

"Let me make this point for Mr Natalegawa's benefit: Indonesian-flagged boats with Indonesian crews are breaking our laws bringing people into our our territorial waters," he told ABC's The Drum.

"This is a breach of our sovereignty and the Indonesians need to understand that, instead of a lot of pious rhetoric about the Australian Government breaching their sovereignty.

"Their people, their boats, their crews are breaching our sovereignty and this is something that needs to be worked out in a mature and constructive way as it was during the Howard years.

"Indonesia has a heavy responsibility to bear in helping Australia solve this problem, not take the view that they can liberally attack the Australian Government and continue to allow their boats with their crews bringing people to our country ... breaking our laws in doing so."

Effective border policy needs Indonesian cooperation: UN

Ms Bishop has previously said she was confident the Coalition would be able to implement all of its asylum seeker policies, regardless of how Indonesia viewed them.

However, the United Nations' refugee agency says the Government will struggle to turn back boats without Indonesian cooperation.

"We don't think you can resolve the issues by unilaterally turning back boats," the UNHCR's regional representative Richard Towle told PM.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Listen Duration: 4 minutes 12 seconds 4 m 12 s UNHCR: Turning back boats will be difficult without Indonesia's co-operation ( Lexi Metherell ) Download 1.9 MB

"Those sorts of things raise enormously challenging problems for people involved in rescue at sea and interceptions ... and without the strong agreement of a receiving country it's very difficult for those things to be done effectively.

"And what worries us in this situation is that it doesn't address the acute protection needs of people who are taking these difficult and dangerous journeys.

"It's very important to address both the legitimate border and security concerns of states but also make sure that people are fairly and humanely treated. And that's the kind of balance we think can be best achieved through genuine long-term strategic engagement with countries in the region."

Morrison to inspect Manus Island centre

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 Mr Abbott 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.