Australian maritime patrols were involved in turning back asylum-seeker boats when they breached Indonesian territory six times, secret government documents reveal.

The disclosure puts an end to two years of speculation that the incursions involved the federal government’s controversial turnback policy.

Previously blanked-out details from the joint Defence and now-defunct Customs and Border Protection Service review of the breaches have been disclosed to AAP after a two-year Freedom of Information battle.

The Office of the Information Commissioner forced the Immigration Department to disclose more information but specific details of the six incidents have been withheld.

The new revelations include:

Confirmation there were 13 boat arrivals in Australian waters between 1 December, 2013 and 20 January, 2014.



When returning six of the boats, Australian naval vessels entered Indonesian waters.



They did not know they were in Indonesian waters because boundaries do not appear on nautical charts.



A directive from the commander of Operation Sovereign Borders to personnel was silent on the conduct of turnback activity within Indonesia’s territorial sea limits.



Headquarters approved patrol plans even though they included details of incursions into Indonesian waters. The miscalculations were not noticed in the approval process or post-operations reporting.



Sailors were trained in “public order management” so they were prepared for non-compliant behaviour of asylum seekers.



A spokesman for the immigration minister, Peter Dutton, declined to comment on the documents on Friday, saying the reports had been publicly canvassed previously.

Australia had to apologise to Indonesia for the unintentional breaches of its waters, which sparked a diplomatic incident. Indonesian warships were moved towards the Australian border following the admission in January 2014.



An Australian navy captain was sacked, a second was sanctioned and five were counselled in the aftermath of the review.

It emerged during the review that a crew member had raised concerns they were heading into Indonesian waters but the officer in charge failed to escalate the information to his chain of command, and continued with the operation.



One of the vessels, the Ocean Protector, had digital maps on board which would have shown the baseline markings, but it was not known if they were switched on at the time. The Ocean Protector incurred nine kilometres into Indonesia’s internal waters – much further than during the other incidents.

The review found no evidence the crew knew the correct location of the baseline, but found “substantial evidence” the calculations used were wrong, a customs spokesman told Guardian Australia at the time.

The review recommended that rules of engagement be reviewed and harmonised for the defence force and Operation Sovereign Borders, the new disclosures show.

The document also quotes parts of the UN Convention on the Law of Sea, which warns there is no “innocent passage” if a vessel is loading or unloading any person contrary to the customs, fiscal and immigration or sanitary laws and regulations of the coastal state.

The confirmation that Australia was conducting turnback operations is likely to further strain Indonesian relations. Following the most recent turnback – involving six Bangladeshi men and two Indonesian crew – the Indonesian government again criticised the policy.

A foreign ministry spokesman, Arrmanatha Nasir, said turnbacks were “dangerous action and not the permanent solution to overcome the problem of irregular migrants”.

Dutton on Friday dismissed the warning and said the two countries had a good relationship and were working together closely.

“We’ve got a good relationship with Indonesia and work closely with them,” “We know there are about 14,000 people who are in Indonesia ready to hop on boats now,” he told media in Melbourne.

Dutton and foreign minister Julie Bishop are scheduled to travel to Indonesia for the Bali process ministerial meeting on combating people smuggling on 22 March.