Australia’s relations with Indonesia have been dealt a further blow with confirmation one or more navy ships went into Indonesian waters without official permission as they were tackling people-smugglers.

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.

Immigration Minister Scott Morrison said he had been advised on Wednesday that there had been a breach or breaches of Indonesian waters during Operation Sovereign Borders – the government’s strategy to “stop the boats”.

“This was done unintentionally and without knowledge or sanction by the Australian government,” Morrison told reporters in Canberra.

The details of the incursions, including which vessels were involved and when the events occurred, are being reviewed by the Chief of the Defence Force David Hurley and Australian Customs and Border Protection Command.

Morrison said Foreign Minister Julie Bishop had apologised to her Indonesian counterpart Marty Natelegawa on Thursday.

It was not revealed how many navy vessels were involved, when the events occurred or how far the vessels went into Indonesian waters.

The minister also declined to say whether the navy ships were in the process of turning back asylum seeker vessels when the breaches occurred.

He said Australia had offered an “unqualified apology” to Indonesia.

“The Australian government takes our shared commitment with Indonesia to mutually respect the sovereignty of each nation very very seriously,” he said.

Steps had been taken to ensure such breaches would not occur again, Morrison said.

Operation Sovereign Borders commander General Angus Campbell said he had been made aware of the incidents when he received a report from Border Protection Command on Wednesday.

He said personnel believed they were still operating outside Indonesian waters at the time and that it was an “innocent error”.

“I’m determined such events won’t occur again,” Campbell said.

Morrison said Australia had a healthy relationship with Indonesia.

“We operate on a no-surprises approach,” he said.

“Having an open and honest relationship and a positive relationship is one where you can raise these type of matters when they occur.”

The minister said he was unaware whether the Indonesian government had launched its own formal investigation.