A senior adviser to the Indonesian government says the country should not accept asylum seekers rescued by Australia as they would be a "social burden" and do not want to return there.

A standoff between Canberra and Jakarta developed late last week over a boatload of about 60 asylum seekers rescued by an Australian ship off the south coast of Java.

The asylum seekers were picked up inside Indonesia's search and rescue zone.

Australian authorities wanted Indonesia to take back the asylum seekers, but the request was refused and the group has since been taken to Christmas Island for detention.

Out of a total of four similar requests to return asylum seekers, two including last week's request have been refused since the Abbott Government was elected.

Immigration Minister Scott Morrison on Monday said the situation was "very frustrating" as there was "no real rhyme or reason to it".

But Professor Dewi Fortuna Anwar, who advises the Indonesian vice-president, says Indonesia is a stepping stone to Australia and asylum seekers should not be made to return.

"They're not Indonesians, the 65 people are coming from the Middle East," she told the ABC's 7.30.

"Our geography is not our choice. Indonesia is on the way to Australia.

"These people pass through Indonesia and the Australian Navy intercepted the boat and then expected Indonesia to take this boat back.

"They would be social burdens to Indonesia. They did not want to come to Indonesia."

Professor Anwar says Jakarta has made it "very clear" that there should be close talks between the two governments on the issue.

"It should not just be one side imposing its will on the others," she said.

She says Australia is a big country with a relatively small population which will always act as a "honey pot for people coming from other countries".

Australia pays deal being discussed

Professor Anwar also revealed talks are underway between Jakarta and Canberra about a deal similar to the previous Labor government's people swap agreement with Malaysia.

She says under the deal, asylum seekers intercepted by Australian authorities could be sent to Indonesia in exchange for refugees.

"If Indonesia were to take them (asylum seekers), the cost of the burdens would be borne by Australia," she said.

"And then at the same time, Australia will take the same number of people that are already sitting in detention centres in Indonesia."

Professor Anwar also says Indonesia does not have the resources to intercept every asylum boat.

"Trying to intercept boats and so on, it would really be putting our resources under a lot of strain," she said.

"So I would think trying to help Indonesia improve capacities to ensure that our waters are safe is fine."

But Indonesia's sovereignty would still need to be respected, Professor Anwar says.

"I don't think it would be acceptable for Australian ships to operate in Indonesian territorial waters," she said.

Abbott says Indonesia should have accept asylum seeker group

Prime Minister Tony Abbott has voiced his frustration at Indonesia rejecting the recent group of asylum seekers.

"These people were in a search and rescue situation in the Indonesian search and rescue zone," he told Macquarie Radio on Monday.

"Now the normal international law is that if you are rescued in a country's search and rescue zone, that country has an obligation to take you."

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 13 minutes 40 seconds 13 m Opposition immigration spokesman Richard Marles speaks to Lateline

But Opposition immigration spokesman Richard Marles says he is not sure that is the right course of action in these circumstances.

He says cooperation is needed on this issue and Indonesia has been consistent in saying they do not want to see boats turned back.

"It doesn't make sense to do something that the Indonesians are not prepared to do," he told ABC's Lateline.

"We can sit here in Australia and tell Indonesia what we think we should and shouldn't do, but in terms of resolving this problem the only way forward is to act cooperatively with Indonesia."

Mr Marles also criticised Mr Abbott for airing diplomatic issues publically.

"This is a government which said that it wasn't going to engage in megaphone diplomacy and yet today we hear our own Prime Minister talking on the airwaves about Indonesian obligations here," he said.