Immigration Minister Scott Morrison on Friday confirmed Australian navy vessels had inadvertently entered Indonesian waters withoutpermission on several occasions.
A spokesman for Indonesia's Co-ordinating Minister for Politics, Securityand Law, Djoko Suyanto, said the development was regrettable, while warning it would have implications for already tense relations betweenJakarta and Canberra.
"If they entered Indonesian waters like that, this will only worsen thesituation and the relationship between Indonesia and Australia," AgusBarnas said on Friday.
"Australia's attitude in this if they really breached the Indonesiansovereign territory is regrettable. As a good neighbour, Australia shouldrespect Indonesia's sovereignty."
Listen: Australia apologises for violating Indonesian waters, Santilla Chingaipe reportsHe said the incident could delay a rapprochement between the countriesfollowing Jakarta's decision late last year to freeze co-operation withAustralia in the wake of the spying row.
"If what the Australian navy did is true, that would only worsen theIndonesia-Australia relationship," he said.
"It could hamper the normalisation of the Indonesia-Australiarelationship."
The minister was aware of the development but was not immediatelyavailable for comment.
It's understood Mr Djoko was set to meet with President Susilo Bambang Yudhoyono later on Friday.
Earlier on Friday, Mr Morrison said the government received informationon Wednesday that Australian authorities had entered Indonesian waters onseveral occasions, in breach of Australian government policy.
"This was done unintentionally and without knowledge or sanction by theAustralian government," he told reporters on Friday.
He said Foreign Minister Julie Bishop apologised to her Indonesiancounterpart Marty Natalegawa on Thursday. Mr Natalegawa was travellingand unable to receive the message personally.
Mr Morrison said a more formal apology will be provided to the Indonesian government via the Australian embassy in Indonesia.
Operation Sovereign Borders commander Lieutenant General Angus Campbell said he was advised of the breach on Wednesday afternoon after a routine report was examined by a border command official.
He said Navy personnel did not know they had breached Indonesian waters at the time.
"I and I am sure all those involved in the conduct of Operation Sovereign Borders regret any affront to Indonesia these events may have occurred," he said.
Opposition Leader Bill Shorten says the government needs to stop blaming the navy and take responsibility for its own border protection policy.
"These service men and women do an extremely tough job under very difficult circumstances and they shouldn't be blamed for the failings of the Abbott government and its policies," Mr Shorten said.
The latest diplomatic skirmish comes amid claims from a group of asylum seekers that they were given a lifeboat by Australian authorities and then sent back to Indonesia under their own steam, after their own boat had earlier become disabled.
The diplomatic ties were already under pressure after claims Australian intelligence officers tapped the mobile phone of Indonesian president Susilo Bambang Yudhoyono and his wife and senior government members.
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