Immigration Minister Scott Morrison is confident there won't be a repeat of Australian border-protection vessels entering Indonesian waters.
A Defence and Customs review has found Australian ships inadvertently entered Indonesian territory six times in December and January.
"On each occasion the incursion was inadvertent, in that each arose from incorrect calculation of the boundaries of Indonesian waters, rather than as a deliberate action or navigational error," the review says.
Mr Morrison described the breaches as accidents.
"It's very clear from the government's policies and operational instructions that operations were to be done only where it was safe to do so and they were not to incur on Indonesian sovereign territory within 12 nautical miles of the archipelagical (sic) baseline," Mr Morrison told Macquarie Radio.
"It was an accident."
He said measures were in place to ensure there were no repeat incidents.
The minister confirmed formal apologies to Indonesia took place weeks ago.
The joint review examines all patrols by navy and customs vessels on Operation Sovereign Borders between December 1 and January 20.
Customs has released only the executive summary of the review, which does not disclose what the Australian vessels were doing when they entered Indonesian waters, or how far they intruded.
There had been speculation they might have been towing back asylum seeker boats.
A range of policies and procedures will now be reassessed, and the chiefs of the navy and customs will consider if there were any lapses in professional conduct.
Training for Australian crews involved in Operation Sovereign Borders will be amended to emphasise staying outside Indonesian waters.
Labor's immigration spokesman, Richard Marles, called for the full report to be released.
"Serious implications remain in terms of our relations with Indonesia," he told AAP.
"The statement released today highlights a systemic problem arising out of this government's border-protection policy."
Australian Greens Senator Sarah Hanson-Young indicated she would demand the full report be tabled in the Senate.