Prime Minister Tony Abbott is refusing to deny claims Australian officials have paid asylum boat crews to turn back to Indonesia, saying the Government will stop the boats "by hook or by crook".

Australian border officials reportedly handed over thousands of dollars to the captain and crew of a vessel carrying 65 asylum seekers which was intercepted off Java last week.

An Indonesian police chief was quoted as saying the six crew members said they had each been given $US5,000 by Australian officials to turn back.

Their vessel later crashed into a reef near the remote Rote Island.

Indonesia's foreign ministry later told the ABC Indonesian police were investigating the claims.

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"This is endangering life. They were in the middle of the sea, but were pushed back," foreign ministry spokesman Arrmanatha Nasir said.

Mr Abbott said on Friday "creative strategies" had been developed to stop the boats.

"What we do is stop the boats by hook or by crook, because that's what we've got to do and that's what we've successfully done," Mr Abbott told Macquarie Radio.

"By hook or by crook we are going to stop the trade.

"I am proud of the work our border protection agencies have done, I really am proud of the work that they've done and they've been incredibly creative in coming up with a whole range of strategies to break this evil trade.

"We will do whatever is reasonably necessary to protect our country from people smuggling and from the effect of this evil and damaging trade."

Mr Abbott would not go into further details about the allegation, saying the Government did not comment on operational matters, and the work of security agencies should not be discussed publicly.

He also sidestepped questions about whether it was acceptable to pay people smugglers, and whether there should be an investigation.

Later on Friday, Mr Abbott did not repeat his "by hook or by crook" description of anti-asylum boat measures, but again did not deny the claims.

"We have stopped the boats. We have used a whole range of measures to stop the boats because that's what the Australian people elected us to do," he said.

"We don't go into the details of the operational measures needed to stop the boats."

A Sri Lankan asylum seeker called Kajuran has told ABC News a similar story, and earlier this week a Bangladeshi named Nazmul Hassan told Radio New Zealand $7,200 was paid to the captain and crew for each passenger.

Mr Hassan said Indonesian authorities later confiscated much of that money.

Navy vessels being used as 'floating ATMs': Labor

Labor's immigration spokesman, Richard Marles, said if payments were occurring, it was a "very dangerous development" that saw Navy vessels become a "floating ATM".

"We need to be reducing the pull factors in this journey," Mr Marles said.

"What kind of a pull factor is it to a people smuggler, knowing that if they encounter an Australian Navy vessel, they will receive an Australian taxpayer-funded cheque?

"People smugglers, their place should be facing prosecution with the full force of the law, not be put in a situation that when they turn up aside an Australian Navy vessel they are, in effect, next to a floating ATM.

"That is an enormous problem. It is a dangerous development, and we need to hear some clarity from this Government today about whether that is the practice they are engaging in."

Greens say Government could be implicated in people trafficking

Greens immigration spokeswoman Sarah Hanson-Young said paying asylum boat crews could be breaking domestic and international law.

"There's a very, very serious question about whether that is a crime, a crime under domestic law, a crime under international law," Senator Hanson-Young said.

"It's a crime to pay people to traffic other individuals. Trafficking, of course, is when someone is paid to take people to a place against their will. These asylum seekers weren't going - didn't want to go back to Indonesia.

"We need a proper, thorough investigation. We need the Prime Minister to start being straight with the Australian people and to identify whether indeed we have Australian officials handing out wads of cash to people traffickers out on the high seas. Either it happened or it didn't. Be upfront about it."

The Prime Minister's comments follow denials this week from senior Government ministers.

When asked whether Australian authorities pay the crew members of people smuggling boats to turn back, Foreign Minister Julie Bishop said: "No".

Immigration Minister Peter Dutton gave the same response when asked whether officials had recently paid an asylum crew to stay away from Australia.