Navy in breach of Jakarta's waters during Operation Sovereign Borders

AN investigation by the Australian Defence Force has confirmed that at least one Royal Australian Navy vessel implementing the Coalition's border-protection policy has breached Indonesian territorial waters.

The Australian has also confirmed border-protection authorities have begun using lifeboats to return asylum-seekers to Indonesia, a method used for a boatload of people intercepted near Christmas Island last week.

During the past week the navy had been investigating allegations made by people-smugglers and asylum-seekers that Australian Border Protection Command vessels had breached Indonesia's 12-nautical mile limit while towing boats back from Australian waters.

They also claimed that crew members mistreated asylum-seekers by holding them against hot engine parts to inflict burns and by withholding food supplies.

All of these allegations were strongly rejected by Defence Force chief David Hurley, Immigration Minister Scott Morrison and the general in charge of Operation Sovereign Borders, Angus Campbell.

They said the Australian personnel conducted themselves professionally and responsibly.

The Australian has confirmed that the navy's examination of records and global positioning system data revealed yesterday that at least one vessel on border-protection duty under Operation Sovereign Borders entered Indonesian waters while returning an asylum-seeker boat.

While the Abbott government has thrown a cloak of secrecy over border-protection operations, two groups of asylum-seekers have claimed in interviews that they were on boats taken back to Indonesia by the navy.

They claimed that some who objected were handcuffed and otherwise restrained and ill-treated.

One boat was said to have been picked up near Darwin on January 1 and towed for five days before being cut loose near Rote Island. Another was said to have been towed back in December.

Naval crews have been caught between the need to avoid breaching Indonesian waters and ensuring that boats they are turning or towing back to that country arrive safely.

In Jakarta, a spokesman for Djoko Suyanto, the Co-ordinating Minister for Politics, Security and Law, said there had not been an Indonesian complaint about any breach of its territorial waters.

"We have no evidence" of a breach, the spokesman said.

He said the Co-ordinating Minister's office was aware of only two asylum-seeker boats turned back by the Australians, which landed on Rote Island on December 19 and January 6.

About 90 people from those boats were being transferred to immigration detention centres in Sumatra, Riau and Central Java, he said. Mr Djoko's office has been given top responsibility for handling the boatpeople dispute with Australia.

The Australian has been told a large lifeboat was used to ferry passengers of a boat en route to Christmas Island back to Indonesia. The boat was intercepted by border protection personnel after being observed by the crew of an RAAF Orion patrol aircraft.

It is unclear whether anyone went into the water at any point, but sources agree the asylum boat was disabled and that the Australian Navy was on the scene.

"The boat was sinking," one source said.

It is understood the boat was deliberately sabotaged by some of the passengers, rendering it unseaworthy.

Customs and Border Protection Command placed the asylum-seekers on a large lifeboat, deemed by the authorities to be a "safe platform", and returned it to Indonesia.

It is not clear whether the boat sailed to Indonesia under its own steam or whether it was escorted by Indonesian officials. Nor is it known how many asylum-seekers were on the boat, nor where the boat eventually landed.

Mr Morrison declined to comment on the incident.

"For operational security reasons, the government does not confirm or otherwise comment on reports of on-water activities in relation to Operation Sovereign Borders or disclose details of any operations," he said.

Mr Morrison also denied reports Customs and Border Protection personnel had fired warning shots into the air as they intercepted an asylum boat, which was reportedly then redirected by Australian authorities back to Indonesia.

"Without commenting on any specific alleged incident, I can confirm that no shots have been fired at any time by any persons involved in Operation Sovereign Borders since the operation commenced," Mr Morrison said.

Two days ago, Lieutenant-General Campbell confirmed the purchase of lifeboats, although he would not say what they would be used for. It was not clear whether the lifeboat used in the operation was one referred to by General Campbell or another craft.

Indonesia's Foreign Minister Marty Natalegawa criticised the Abbott government's apparent intention to put asylum-seekers into lifeboats and escort them back to Indonesia as "a slippery slope".

Dr Natalegawa's comments suggest the Indonesians will take an even dimmer view of using lifeboats than they do of turning back fishing boats carrying asylum-seekers.

"It's one thing to turn back the actual boats on which (asylum-seekers) have been travelling but another issue when they have actually been transferred to another boat and actually been facilitated and actually told to go that direction," he told the ABC.

"To be zeroing in on issues ... in a manner that tends to divide is not helpful."

Last week's incident is the first known occasion when lifeboats were used to ferry asylum-seekers back into Indonesian waters.

Bill Shorten said he respected the work of ADF personnel but he attacked what he said was a government "culture of secrecy".

"I don't want to see Australian servicemen and servicewomen caught up as the meat in an Abbott-Morrison secrecy sandwich on our boats," the Opposition Leader said.

The government has offered Labor's immigration spokesman Richard Marles and Mr Shorten a full briefing on progress in Operation Sovereign Borders - an offer to be taken up when parliament resumes next month.

Additional reporting: Paige Taylor, Peter Alford