Australia has apologized to Indonesia over Australian border patrol boats entering Indonesian territorial waters without permission as part of a bid to stop asylum seekers.

The boat patrols had the potential to further damage strained relations between the near neighbors. Indonesia was outraged and downgraded its relations with Australia two months ago over the alleged bugging of phones belonging to President Susilo Bambang Yudhoyono, his wife and members of his inner circle in 2009.

Border Protection Minister Scott Morrison said a formal apology on behalf of the Australian government would be made by Australia's embassy in Jakarta on Friday.

Australia's navy chef had already apologized to his Indonesian counterpart and Australia's foreign minister had unsuccessfully attempted to contact her Indonesian counterpart to apologize, Morrison said. Indonesian Foreign Minister Marty Natalegawa was overseas on business.

Morrison described the breaches which he became aware of on Wednesday as "a very serious matter," which he said was "extremely regrettable."

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

Indonesia has complained that Australia's policy of turning back asylum seekers' boats threatened to violate Indonesian sovereignty.

Australia has denied this, saying that Australian vessels would not enter Indonesia's territorial waters when turning boats around. The government has refused to say whether it has even implemented the policy, drawing accusations of excessive secrecy surrounding its new stance on asylum seekers.

Prime Minister Tony Abbott's government was elected in September last year on a promise of tough new measures to stop asylum seekers from countries such as Iran, Afghanistan and Myanmar reaching Australia in rickety Indonesian fishing boats.

The numbers has soared in recent years, although the government announced this week that there had been no new arrivals in more than three weeks.

Lt. Gen. Angus Campbell, who as commander of Operation Sovereign Borders oversees Australia's efforts to stop boats full of asylum seekers traveling from Indonesian ports, said he became aware on Wednesday that Australian vessels had traveled through Indonesian water "on several occasions."

He would not say how many vessels were involved, or where and when the breaches took place.

He said the breaches had been brought to his attention by an Australian official.

"I regret, and I'm sure all those involved in the conduct of Operation Sovereign Borders, regret any affront to Indonesian that these events may have caused," Campbell said.

Morrison disclosed the breaches after The Australian newspaper reported on Friday that an Australian defense investigation had revealed that at least one navy vessel implementing border protection policy had breached Indonesian territorial waters.

Popular

Great Barrier Reef hit by record bleaching

Govt to undo latest curbs on personal imports

Middle East on edge as Israel and Iran trade threats