Australia's backdown from a stalemate with Indonesia over the turn-around of an asylum seeker boat signals a crack in the government's border protection policy, critics say.

But Prime Minister Tony Abbott insists the coalition's plan to stop the boats is working despite there being setbacks.

Immigration Minister Scott Morrison on Saturday ordered an end to a stand-off lasting more than 24 hours, where a suspected asylum seeker boat carrying more than 50 people had been intercepted by Australian authorities off the coast of Java.

Indonesia refused requests for the passengers to be taken ashore, leaving the boat people in limbo at sea under the watch of the Australian navy.

"In the best interests of the safety of the passengers and crew ... earlier this morning I requested (the) transfer (of) the persons rescued to Christmas Island," Mr Morrison said in a statement on Saturday.

Australian authorities had responded on Thursday to a distress call from the wooden boat which was subsequently located in Indonesia's search and rescue zone.

"On two recent occasions, Indonesia has agreed to these requests and facilitated an on water transfer," Mr Morrison said of the turn back attempt.

But in the latest case, Indonesia said they would "review" the situation.

"What is absolutely clear from the events of today is that the boats are not being turned back, indeed the boats are coming to Christmas Island," opposition immigration spokesman Richard Marles said.

"The border protection policy which Tony Abbott took to the election is in tatters."

But the prime minister defended his government's approach.

"We said that we'd stop the boats, and while they have not yet stopped, they are slowing and they are stopping," Mr Abbott told reporters on Saturday.

"We will have setbacks and we will have disappointments, but we will succeed."

The prime minister refused to comment on "operational matters" relating to the latest boat interception but Mr Morrison confirmed that all passengers had been accounted for and would be taken to detention centres at Manus Island or Nauru after initial processing at Christmas Island.

The Australian Greens have called on the government to end its secrecy over border security operations, outlining plans to move a motion in parliament next week compelling the government to release details.

"Mr Abbott's excuses for secrecy are wearing thin and the Greens will use the powers of the Parliament to reinforce transparency," the minor party's immigration spokeswoman Sarah Hanson-Young said.

"The Coalition's turnaround policy is in tatters and it is time that Mr Abbott admitted that he had it wrong from the start."

Reports from Indonesia say there were some 63 people on the latest asylum seeker boat.

An Indonesia government spokesman said Jakarta was reluctant to accept the passengers because the boat was in working order when detected and the asylum seekers were not in danger.