Jakarta yesterday 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.
The response 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 Canberra would pursue its hardline policies to halt asylum-seeker boats.
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.
Jakarta said it would "intensify its maritime patrols", sending an extra naval ship to patrol its southern maritime borders around the island of Timor.
Morrison earlier said the government learnt on Wednesday that the Australian vessels had entered Indonesian waters on several occasions.
Morrison said Australia "deeply regrets" the breaches of territorial sovereignty but at the same time maintained Australia's right to protect its own borders.
"We have offered the apologies. We have been very clear about what has occurred both with Indonesia and here today," he said. "But we won't let this setback get in the way of the job we were elected to do, which is stop the boats."
Senior Australian diplomat David Engel later visited the Foreign Affairs Ministry in Jakarta and formally conveyed his country's apology.
Indonesia downgraded its relations with Australia in November as a result of the spying allegations, suspending intelligence and military co-operation, including over asylum seekers.
A protracted crisis between the often uneasy neighbours could have serious repercussions. Indonesia is a major importer of Australian agricultural products such as wheat and live cattle.
The number of refugees reaching Australia pales in comparison with other countries but it is a polarising political issue that also stokes tension with Indonesia over border policies that have been criticised by the United Nations and international human rights groups. Prime Minister Tony Abbott's conservative government came to power after its tough campaigning against asylum seekers and an easing of border policies by the former Labor government that preceded a rise in the number of boats.
Its policies include offshore detention centres that hold thousands of asylum seekers, many of whom have fled conflicts in Afghanistan, Darfur, Pakistan, Somalia and Syria.
Additional reporting by Reuters