There is growing frustration in senior Government ranks about Indonesia's handling of asylum seeker boats, with Immigration Minister Scott Morrison saying "there's no real rhyme or reason to it".

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.

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.

"It's very frustrating... there's no real rhyme or reason to it, necessarily," Mr Morrison told Macquarie Radio this morning.

Opposition immigration spokesman Richard Marles leapt on the statement as a diplomatic foul-up.

"That is an astounding comment to make in relation to foreign affairs," he said.

"In foreign affairs, words are bullets."

Mr Morrison added that the media coverage of the standoff made the situation more difficult, with Indonesian officials being quoted in the Jakarta Post over the weekend.

"This last instance became very problematic because it went very public," he said.

"That's why we've been so careful in our public comments not to run that sort of a commentary.

"I gave an undertaking to the Indonesians that when we would deal on these issues, we'd do it directly and we'd do it discreetly."

Indonesia has refused past Australian requests

On two previous occasions, according to Mr Morrison, Indonesia did agree to take back asylum seekers who had been picked up by Australian ships.

"And on one occasion they didn't but on that occasion we were a much further distance away than we were on this most recent occasion," he said.

Impasse a testing time for Australian diplomacy It is a challenging time for Australian - Indonesian relations with the problem intensified due to the recent spying revelations and Australia's refusal to confirm, deny or apologise. But as the political argument intensifies in Australia over who's to blame, it is worth looking objectively at the accuracy of what both sides of Australian politics are saying. The current standoff over the policy of 'turning back the boats' was inevitable because in Opposition Tony Abbott over promoted his ability to achieve the objective of Indonesian cooperation. And Indonesia never liked the idea anyway. It was always going to have problems. But as the Opposition attacks the Government remember that the former Gillard Labor Government offended Indonesia and brought relations to an impasse over its unilateral decision to ban live beef exports. Deputy Opposition leader Tanya Plibersek's claim "the Abbott Government has turned the once strong relationship with Indonesia sour" needs to be taken with a grain of salt. Labor didn't perform well in Government in its relations with Indonesia. As former Ambassador Bill Farmer said in a speech in Melbourne several months ago the decision to halt beef exports was 'ill conceived' and a '10 out of 10 with how not to deal with Indonesia.' Over the years Australian politicians haven't found it easy to deal with Indonesia and they are not finding it easy now. - Asia Editor Catherine McGrath

"On some occasions it'll happen, on other occasions it won't."

Prime Minister Tony Abbott has suggested that Indonesia had an obligation to accept the asylum seekers.

"These people were in a search and rescue situation in the Indonesian search and rescue zone," he said.

"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.

"You can go to the nearest port and the nearest port is normally the port that is in the country whose search and rescue zone you've been picked up in."

But Mr Abbott played down the significance of the standoff.

"We have good and improving relations with Indonesia on this and I wouldn't want to make too much of what did or didn't happen on Friday," he said.

"We will continue to do our job to uphold the ordinary law of the sea and I think other countries will do theirs."

Mr Morrison says Indonesia lacks the resources to rescue boats in trouble in its southern waters.

"They don't have a capability on their southern coast largely to effect search and rescues, this is the frustrating element of this," he said.

Indonesia disputes whether the boat was within its search and rescue zone.

Coalition confident asylum seeker policies will continue

As the standoff unfolded, 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.

But the Government insists its asylum seeker policies have not been scuttled and the Prime Minister says relations with Indonesia are "good and getting better all the time".

The Government is also refusing to confirm reports that two more asylum seeker boats were intercepted over the weekend.

A spokesman for Mr Morrison released a statement saying that "updates on Operation Sovereign Borders, including boat arrivals are provided at weekly briefings".

Labor's Mr Marles says the minister is not keeping the public informed.

"Today we have a situation where the Australian people are learning more about Operations Sovereign Borders from the Jakarta Post than they are from their own government," he said.

"That is a situation that simply needs to stop."

Mr Morrison says boat arrivals have decreased by 75 per cent under the Coalition.