An Australian warship that entered Indonesian waters while pushing back an asylum seeker boat ignored repeated warnings from a nearby patrol boat that it was in foreign waters.
The military took the extraordinary step last week of removing the captain of the warship from his command for breaching Indonesian territorial waters as part of the Federal Government's operation sovereign borders.
An inquiry found Royal Australian Navy and Customs vessels strayed into Indonesian waters six times in efforts to turn back or tow back boats in December and January.
The incursions were despite captains getting orders not to go within 12 nautical miles of Indonesia.
The West Australian believes the captain of one vessel was cautioned by another Australian crew he was inside Indonesia's 12-mile limit.
But the commander is said to have checked his instruments and replied he was sure his vessel was still in international waters.
Two of Australia's most modern vessels were involved in incursions - the Anzac class frigates HMAS Parramatta and HMAS Stuart.
Another commander was "administratively sanctioned" and a further five officers are to be formally or informally counselled.
The disciplinary actions have raised eyebrows in sections of the military, with naval personnel complaining the officers were unfairly punished for executing a controversial Government policy.
But senior Defence figures remain firm the officers broke clear guidelines and action was needed.
Indonesian officials claimed last week the Australian Government had reassured them the policy of turning back asylum seeker boats had been quietly killed off.
But Immigration Minister Scott Morrison said yesterday there had been no change in border security operations.