Prime Minister Tony Abbott has refused to say whether Australian officials handed over cash payments on the high seas to people smugglers, despite two cabinet ministers denying the allegations and the Indonesian government launching an investigation.

Labor and the Greens have called on Mr Abbott to come clean on the claims, saying that if they are true any such payments are encouraging the very people the government calls "evil" to be lured to customs vessels for cash from a "floating ATM".

In a radio interview on Friday, Mr Abbott said the government stopped the boats "by hook or by crook", but refused to say whether it would investigate the allegations or whether they were true. He did say border protection agencies were "incredibly creative in coming up with a whole range of strategies to break this evil trade".

In a later press conference, he again refused to deny the allegations, saying: "Every time we comment on operational matters we give information to our enemies. We give information to people who want to do the wrong thing by our country."

Labor immigration spokesman Richard Marles said that if the claims were true, Australia was providing an incentive to people smugglers and creating a "pull factor" for more boats to try to make the journey to Australia.

"It is absolutely incumbent on the government to tell the Australian people where the truth lies," Mr Marles said. "We need to know if the Australian government is paying people smugglers.

"That is a very dangerous development indeed," he said. "People smugglers should be facing prosecution with the full force of the law."

Mr Marles said people smugglers should not be pulling up to customs vessels with the expectation they are a "floating ATM".

Asylum seekers and the Indonesian police chief claim Australian officials gave each crew member $US5000 (A$6500) to take a boat to Indonesia. The Indonesian government is investigating the claims, saying they could amount to "bribery" or "even people smuggling".

Human Rights Law Centre executive director Hugh de Kretser said the allegations left Australia open to breaching a number of laws, and that the secrecy from the government was "extraordinary".

"If true, there are serious questions about whether these payments breach Australian law, Indonesian law and international law," he said.

"It's a sad indictment against the state of our democracy that we are learning more about these critical human rights issues from Indonesia than from Canberra."

Greens immigration spokeswoman Sarah Hanson-Young said the Prime Minister needed to "come clean" on whether the government had engaged in trafficking.

"The Prime Minister has all but admitted that the government is prepared to do anything out on the high seas, even it seems that means breaking the law or participating in people trafficking," she said.

A spokeswoman for the United Nations High Commissioner for Refugees said it was concerned by "any policy practice that involved pushing asylum seeker boats back to sea without a proper consideration of individual needs for protection and respect for human rights."

Earlier this week Foreign Minister Julie Bishop and Immigration Minister Peter Dutton both denied Australian officials had made payments to the crew.

When Ms Bishop was asked on Wednesday whether Australian authorities ever paid people to return asylum seekers she replied: "No."

A spokeswoman also said Indonesian authorities had not been in contact with Ms Bishop regarding the alleged payments.

Mr Dutton also replied "No" when asked whether Australian officials paid the crew and captain of a boat carrying asylum seekers to take them away from Australia recently.

In the press conference, Mr Abbott was asked whether he supported both of his cabinet ministers denying the claims.

"Of course, I always stand by my ministers," he said.