The Indonesian government has distanced itself from the claims of a senior adviser who said an asylum seeker deal is being discussed with Australia.

Dr Dewi Fortuna Anwar had said there were discussions underway about exchanging asylum seekers picked up by Australian ships for refugees held in Indonesian detention centres.

However Djoko Suyanto, Indonesia's coordinating minister for security and political affairs, has told the ABC that Dr Anwar "is not the person in charge for this issue".

"She is not the right person to talk about the asylum seeker issue," he said.

He says he has been appointed by president Susilo Bambang Yudhoyono as the official authority, and that there is no asylum seeker deal.

In a statement sent to ABC via text message, he went on to clarify Indonesia's position on asylum seekers.

Djoko Suyanto: - The destination of these asylum seekers is Australia, NOT Indonesia. - The Indonesian government is also experiencing the same problem about these asylum seekers, whose destination is Australia. At the moment many of them are detained in Indonesian immigration [detention centres]. - Each country has its own detention centres for these asylum seekers, so those asylum seekers should be taken to the detention centres of each country for further process[ing]. - It's the modus operandi of these asylum seekers to ask to be rescued by Australian ships - because Australia is their destination country, NOT Indonesia. - The Jakarta Declaration 2013, which was attended by [the] related foreign ministers that deal with the asylum seekers issue, requires the involvement of the origin countries of these asylum seekers, not only the transit countries' involvement. - The Indonesian government has also established marine and land task forces for prevention operations and law enforcement. - The Indonesian government policies have been executed since previous Australian governments.

Last week Djoko Suyanto said Indonesia's position on asylum seeker returns had remained the same since the Rudd government and would not change under the Government of Tony Abbott.

In another text message he also said Indonesia had "never agreed" to Australia's wishes and policies on the matter.

Australia 'continuing to pursue' possible Indonesia cooperation

Sorry, this video has expired Government denies negotiating a refugee swap deal with Indonesia ( Greg Jennett )

The Australian Government has said it is not negotiating "people swap" deal with Indonesia, but is exploring other avenues of cooperation.

Immigration Minister Scott Morrison yesterday released a statement saying the Government "will continue to pursue all areas of possible cooperation" with Indonesia.

But he stated clearly that "the Australian Government is not engaged in people swaps".

"Our discussions are about handling of passengers rescued at sea, and ensuring people are taken to a place of safety as soon as possible," he said.

"We will continue to undertake these discussions directly with Indonesia, and honour our commitments to protect the confidences of these discussions."

Mr Abbott said he did not want to negotiate with Indonesia "through the media" but said talks were underway about the fate of rescued asylum seekers.

He again suggested that Indonesia had an obligation to accept a group of asylum seekers who were rescued last week.

"Obviously under normal search and rescue rules, people who are picked up in a country's search and rescue zone go to the nearest safe port in that country, but we're discussing this with Indonesia," he said.

Opposition Leader Bill Shorten would not say if he supported the prospect of "people swaps" with Indonesia.

"I support working with Indonesia, not telling them what to do," he said.

"This patronising paternalistic attitude to me is breathtaking. What are the Government hiding? We all know that their policy's in tatters."

In 2011, then prime minister Julia Gillard announced Australia had struck a so-called people swap deal with Malaysia to send 800 asylum seekers there in return for taking 4,000 refugees.

The Coalition argued against the arrangement, protesting that Malaysia was not a signatory to the UN Refugee Convention.