Australian Prime Minister Tony Abbott has reaffirmed his determination to continue turning asylum seekers' boats back to Indonesia, despite warnings of naval conflict at sea, allegations of brutality and new criticism by human rights watchdogs.

Relations with Indonesia have been sorely stretched by revelations of Australian spying and Abbott's unflinching hard line on asylum seekers in the face of anger in Jakarta.

Canberra has been forced to apologise for a number of what it says were "inadvertent" incursions into Indonesian waters by Australian vessels, but so far there has been no official response from Jakarta. Indonesia has sent more ships to patrol its waters to "protect its sovereignty and territorial integrity".

An inquiry involving the Navy and Customs is now under way to identify "any procedural weaknesses or deficiencies" in maritime operations.


Abbott said yesterday that Australia would "continue to do what we are entitled to do to secure our borders".

"Stopping the boats is a matter of sovereignty and President [Susilo Bambang] Yudhoyono, of all people, ought to understand just how seriously countries take their sovereignty."

Abbott has also been hit with further allegations of mistreatment of intercepted asylum seekers by the Navy, with the ABC airing footage of a number receiving treatment for burns to their hands. Indonesian police told the ABC seven of the 10 treated had severe burns and that they had been told Australian Navy personnel had forced them to hold hot exhaust pipes on their intercepted vessel.

One asylum seeker, Somalian Merke Abdullah Ahmed, said other passengers had been punched: "Some of the passengers on board, they tried to complain and speak about just their problems. They just punched them."

Immigration Minister Scott Morrison angrily rejected the allegations yesterday, saying the claims were unsubstantiated and untrue: "The Australian Government is not going to put up with people sledging the Australian Navy ... I won't have a bar of it."

He said he accepted assurances that Navy and Customs officers acted properly and that people smugglers were trying to discredit border control operations. "People smugglers have very strong motivations because we are destroying their business," Morrison said.

Tubagus Hasanuddin, a former Indonesian general who now sits on the parliamentary defence, foreign affairs and intelligence commission, told the ABC he did not think the Australian incursions were unintentional and could lead to conflict. "I studied in Australia, in the military academy. The Australian Navy doesn't have wooden boats, they have warships equipped with modern technology. They should have known which part of the water is Indonesia and which is not."

Hasanuddin said tensions would increase if Australia kept turning back the boats: "It's not impossible a clash between Indonesia and Australia national forces, and I believe that this needs to be avoided. It can't happen."

Ousted Labor Prime Minister Kevin Rudd gave similar warnings during the campaign for last year's election, but most analysts do not believe either navy would allow tensions to develop into conflict at sea.

The latest Human Rights Watch annual report said Australia had consistently undermined refugee rights and protections with "scare-mongering politics" placed above the nation's international obligations. Federal Human Rights Commission President Gillian Triggs yesterday attacked the policies of Labor and the Coalition as "extremely harsh and egregious", especially the detention of children. Urging the transfer to Australia of all detainees at centres on Nauru and Papua New Guinea's Manus Island, Triggs said: "Australia cannot avoid its international human rights obligations by transferring asylum seekers to third countries and may remain liable for the consequences of doing so."