Scott Morrison admits Australia breached Indonesian waters

The Abbott government has admitted Australia breached Indonesian territorial waters during operations to deter asylum seeker boats.

Speaking at a press conference in Canberra Immigration Minister Scott Morrison said this was against Australian government policy.

At least one Australian border protection boat "inadvertently" entered Indonesian territorial waters - breaching Indonesia's sovereignty - several times.

"I should stress that this occurred unintentionally and without knowledge or sanction by the Australian government," Mr Morrison said.

Mr Morrison, who said he was notified of the breaches on Wednesday, described the incidents as an operational failure.

He said Australia has informed Indonesia and apologised.

Despite the government's admission that it had entered Indonesian waters, the Immigration Minister said this could not be taken as confirmation Australia was turning back boats.

"It's not for me to confirm or not confirm your assumptions," he said. "What I can say is the Australian government's policies to stop the boats are working and they will continue."

Operation Sovereign Borders Commander Angus Campbell said that Australian personnel believed they had been operating in Australian waters.

"This is a very serious matter," he said.

Lieutenant General Campbell said he had ordered a review into the mistake.

He said he believed the breach occurred on "more than one day" but would not provide more detail on the timing, saying the review needed to look at the issue "without prejudice".

Lieutenant-General Angus Campbell and Immigration minister Scott Morrison. Picture ANDREW MEARES

Lieutenant-General Angus Campbell and Immigration minister Scott Morrison. Picture ANDREW MEARES

"I'm sure all those involved in the conduct of Operation Sovereign Borders regret any affront to Indonesia these events may have caused," he said, telling reporters in Canberra that the mistake would never happen again.

Lieutenant General Campbell suggested - but did not confirm - that more than one boat had been involved in the breaches. 

When asked to clarify how many boats were responsible, he talked about the "passage of a vessel or vessels on several occasions".

Mr Morrison said that Australia's navy chief Ray Griggs phoned his Indonesian counterpart late on Thursday to tell him about the breach and apologise.

Foreign Affairs Minister Julie Bishop has also tried to speak to Indonesian Foreign Minister Marty Natalegawa, to offer an "unqualified apology".

"This has occurred, it's regrettable and we've made the appropriate apologies," Mr Morrison said.

Mr Morrison also described the breach as a "setback" for Operation Sovereign Borders.

"We don't let this setback get in the way of the job we were elected to do which is to stop the boats. So that job continues with full steam ahead and full commitment," he said.

Lieutenant General Campbell said Australian authorities realised the mistake after looking at a routine vessel report.

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