Australia has given in after Indonesia refused to accept asylum seekers who were rescued two days ago off the coast of Java.

Immigration Minister Scott Morrison has confirmed the group of asylum seekers Australia was attempting to return to Indonesia will now be taken to Christmas Island.

Indonesia says roughly 60 asylum seekers were on board a boat which ran into trouble off Java on Thursday.

Mr Morrison says the Government asked Jakarta to transfer them to Indonesia given their boat ran into trouble in Indonesia's search and rescue zone.

It is understood Indonesia yesterday refused Australia's attempt to convince Jakarta to take the group back.

Mr Morrison has released a statement today saying the asylum seekers will not be resettled in Australia.

"While we welcome Indonesia's review of our request, in the best interests of the safety of the passengers and crew of the rescued vessel and the Australian vessel that has been rendering assistance, earlier this morning I requested Lieutenant General Campbell to transfer the persons rescued from the SAR incident to Christmas Island for rapid onward transfer to Manus Island or Nauru," he said.

Yesterday, the Indonesian government declared it would not take back asylum seekers rescued by Australian ships, putting the Coalition's "turn back the boats" policy in jeopardy.

Mr Morrison yesterday rejected suggestions of a standoff.

"We're not going to go into the micro-detail of these operational matters," Mr Morrison said.

Under the Government's new media policy it will only talk about border protection issues at weekly briefings.

PM deflects questions on Indonesian refusal

Prime Minister Tony Abbott used a speech in Perth today to declare the country's relationship with Indonesia is improving and vowed to stop asylum seeker boats coming to Australia.

"We have good relations with Indonesia, good and improving relations, but we will stop these boats," he said.

"We will stop these boats in any test of will between the Australian Government and the people smugglers. We will and we must prevail."

He told reporters the latest transfer of the 60 asylum seekers to Christmas Island is in line with Government policy.

"What this signals is that Government policies are in place and the boat people in question, the illegal boat people in question, will go swiftly to Manus Island or Nauru."

He also deflected questions about why Indonesia refused the request.

"I'm not going to comment on operational matters, it's not our practice to comment on operational matters. That just helps the people smugglers," he said.

Labor's immigration spokesman Richard Marles says it was inevitable Australia would have to back down from its policy to turn back asylum seeker boats.

"The diplomacy of the Abbott Government with Indonesia around asylum seekers has been absolutely inept," he said.

"We all know that when it comes to our interactions with Indonesia around asylum seekers they have to be based on cooperation."

'No excuse' for lack of information

Professor Tim Stephens, from the University of Sydney, says there is no excuse for the lack of information on the issue from the Government.

"I think it's highly regrettable that the Government is not releasing information," he said.

"There's no operational reason why they shouldn't release this public information, particularly in circumstances where it's a search and rescue."

A senior government source has told the ABC's AM program there are very good reasons not to share more details.

The Government has publicly said it is because it would put the operation at risk.

Professor Stephens says he cannot see how releasing the information would compromise the operation.

"I can't see how it would change the behaviour of potential future people smuggling operations, if that's what this is," he said.

"So, no, when it comes to search and rescue, ordinarily, information is pooled and the more information that's released, is really the better."