Indonesia has condemned Australian naval incursions into its waters, calling them a "violation of its sovereignty".

It demanded on Friday that Australia suspend its military-led operation to stop the flow of asylum seekers reaching its shores, after Canberra apologised for intrusions by its navy into Indonesian waters.

Jakarta also pledged to increase navy patrols in its southern maritime borders around the island of Timor.

Australian Immigration Minister Scott Morrison expressed regret after revealing that navy vessels had "inadvertently" violated Indonesian waters during border security operations.

"We will ensure that the issues that led to these inadvertent breaches of Indonesian territorial sovereignty are rectified and do not reoccur," he said.

However, he said the government would pursue its hardline policies to halt asylum seeker boats.

Simmering Tensions

Asylum seekers arriving on unauthorised boats in Australia, often via Indonesia, are a sensitive issue for both sides, and Canberra's operation to clamp down on them has raised concerns in Jakarta.

The revelations about the Australian naval incursions added to tensions between the neighbours, already strained by a row over spying, with Jakarta responding furiously.

The ministry for political, legal and security affairs issued a statement saying that the naval incursions "constitute a serious matter in bilateral relations of the two countries".

The ministry also demanded a halt to Operation Sovereign Borders until assurances were received there would not be a repeat of such violations.

Lieutenant General Angus Campbell, who heads the operation, refused to explain what the vessels were doing, citing "operational reasons".

Dealing with asylum seekers

Under the new government's policy, not only are asylum seekers arriving by boat sent to Pacific island camps for processing with no chance of settlement in Australia, but boats intercepted at sea can be turned back to Indonesia. 

Australia's policy has been characterised by a near blackout on events at sea, with arrivals falling by more than 80 percent since the Liberal-National government won power in September.

Australia's military chief of staff and the head of border protection would lead a review of the violations, Morrison said, as reports emerged that the navy had started using lifeboats to return asylum seekers to Indonesia.

Source: AFP