The disclosure puts an end to two years of speculation 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 December 1, 2013 and January 20, 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.
Australia had to apologise to Indonesia for the unintentional breaches of its waters.
An Australian navy captain was sacked, a second was sanctioned and five were counselled in the aftermath of the review.
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.
Immigration Minister Peter Dutton and Foreign Minister Julie Bishop are scheduled to travel to Indonesia for the Bali Process ministerial meeting on combating people smuggling on March 22.
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