Aust apologises to Indonesia over breach

Immigration Minister Scott Morrison says the government has apologised to Indonesia after Australian authorities "inadvertently" breached Indonesian territorial waters while conducting border protection operations.

Mr Morrison said on Friday that the government received information on Wednesday afternoon that Australian authorities had entered Indonesian waters on several occasions, in breach of Australian government policy.

"This was done unintentionally and without knowledge or sanction by the Australian government," he told reporters in Canberra.

He said Foreign Minister Julie Bishop apologised to her Indonesian counterpart Marty Natelegawa on Thursday.

The embarrassing breach was revealed during an investigation of allegations made by people-smugglers and asylum-seekers about the behavior of the Navy when conducting operations. 

It was also claimed that Australian crew members had held asylum-seekers against hot engine parts to inflict burns and withheld food supplies and The Australian also reports authorities have used lifeboats to return asylum-seekers to Indonesia.

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