Australia has apologised to Indonesia over its border patrol boats entering the country's territorial waters without permission during a bid to stop asylum seekers.
The boat patrols had the potential to further damage strained relations between the near neighbours. 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.
Australia's navy chef had already apologised to his Indonesian counterpart and the foreign minister had unsuccessfully attempted to contact her Indonesian counterpart to apologise, Mr Morrison said. Indonesian foreign minister Marty Natalegawa was overseas on business.
Mr Morrison described the breaches which he became aware of on Wednesday as "a very serious matter" and "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," he said.
Indonesia has complained that Australia's policy of turning back asylum seekers' boats threatened to violate Indonesian sovereignty.
Australia has denied this, saying its 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 travelling from Indonesian ports, said he became aware on Wednesday that Australian vessels had travelled through Indonesian water "on several occasions".
He would not say how many vessels were involved or where and when the breaches took place.
"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," he said.
Mr Morrison disclosed the breaches after The Australian newspaper reported that an Australian defence investigation had revealed that at least one navy vessel following border protection policy had breached Indonesian territorial waters.