JAKARTA (AFP) -- Indonesia on Friday demanded Australia suspend its military-led operation to halt the flow of asylum-seekers in a furious response after Canberra apologised for intrusions by its navy into Indonesian waters.

Jakarta also pledged to step up navy patrols in its southern maritime borders, saying it "deplores and rejects the violation of its sovereignty" caused by the Australian incursions.

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

However he pledged the government would pursue its hardline policies to halt asylum-seeker boats.

Asylum-seekers arriving on unauthorised boats in Australia, often via Indonesia, are a sensitive issue for both sides, and Canberra's military-led Operation Sovereign Borders 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 Australia's Operation Sovereign Borders until assurances are received there will not be a repeat of such violations.

"Indonesia demands that such operations conducted by the Australian government that led to this incident be suspended until further clarification is received," it said.

Jakarta said it would "intensify its maritime patrols", sending an extra naval ship to patrol its southern maritime borders around the island of Timor.

The ship will join three Indonesian naval vessels already operating in the area, ministry spokesman Agus Barnas said.

Morrison earlier told reporters the government learnt Wednesday that the Australian vessels had entered Indonesian waters on several occasions.

"I should stress this occurred unintentionally and without knowledge or sanction by the Australian government," he said.

He said that Australian Foreign Minister Julie Bishop on Thursday night offered her Indonesian counterpart Marty Natalegawa "an unqualified apology on behalf of the Australian government for inadvertently entering Indonesia's territorial waters".

She also gave "an assurance that such a breach of Indonesian territorial waters would not re-occur", he said.

Charge d'affaires at the Australian embassy in Jakarta, David Engel, went to the Indonesian foreign ministry to offer a formal apology on Friday afternoon.

"We've had a constructive, cordial meeting," he told reporters afterwards.

Lieutenant General Angus Campbell, who heads the operation to stop asylum-seekers arriving in Australia by sea, refused to detail what the vessels were doing for "operational reasons".

But the Australian newspaper reported the navy had been pushing back an asylum-seeker boat at the time.

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.

Even after the incursions, Morrison insisted there would be no change in Australia's policy, which has been characterised by a near blackout on events at sea.

"Despite the unintentional entry of Australian border protection assets into Indonesian territorial waters, our operations that are stopping the boats will continue," he said in a statement.

With no-one who has arrived illegally by boat being transferred to Australian immigration authorities since December 19, it was the first time in more than five years that no asylum-seekers had arrived at this time of the year, he added.

Arrivals have fallen 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 front a review of the violations, Morrison said, as reports emerged that the navy had started using lifeboats to return asylum-seekers to Indonesia.

The Sydney Morning Herald detailed allegations from asylum-seekers now back in Indonesia that the navy had tricked 56 of them into boarding a lifeboat in the belief they were being taken to Australia's Christmas Island.