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".