The Chief of Navy, Vice-Admiral Ray Griggs, said in a statement on Thursday that he believed the incursions in December and January were inadvertent, but that they were not up to the standard of a navy commander.

Five other ship captains will be counselled. Seven navy ships were involved in the six breaches of Indonesia's maritime boundary, which infuriated Jakarta and caused the Abbott government acute political embarrassment.

"There were, in the Chief of Navy's view, lapses in professional conduct that required action to be taken," the statement reads.

As a result, Admiral Griggs would ''remove one Commanding Officer from his command and another will be administratively sanctioned".

It is understood that the administrative sanction will be in the form of a formal warning and reprimand.

“Each of the Commanding Officers conducted these activities with the best of intent. However, I expect nothing but the highest standards of those in command,” Admiral Griggs said.

It is understood at least some of the incursions happened while asylum-seeker boats were being turned back to Indonesia. A review of the incidents by Defence and Customs found that the breaches were inadvertent and arose because the ships' crews did not know where the maritime boundaries lay.

Indonesia, as an archipelago country, has boundaries that are calculated according to base lines, meaning the actual boundary can be much further out than the standard 12 nautical miles.

Citing the Privacy Act, the navy is not giving the names of the ships' commanders, nor of the ships themselves.

Furthermore, the statement does not explicitly state why the punishments differ across the seven ship captains involved, though it says that Admiral Griggs had "carefully considered the circumstances of the positioning of each ship" – indicating the captain stripped of his command had made more grievous errors than the others.

Admiral Griggs added that the actions he was taking were ''not punitive in nature but are aimed solely at upholding the professional standards that the Royal Australian Navy is renowned for and that are necessary for it to undertake its mission''.

He said personal accountability was ''a key feature of Navy’s cultural change program''.

A spokesman for Defence Minister David Johnston declined to comment, saying it was a matter for the navy. It is understood the punishment decision was taken wholly by Admiral Griggs and was made independent of the government.

Labor's acting defence spokesman, David Feeney, said it was ''unfair in the extreme that navy officers are being disciplined and counselled, while Tony Abbott and Scott Morrison refuse to take any responsibility for the Indonesian incursions''.

While stressing he was not criticising Admiral Griggs, Senator Feeney said the key issue was that the government had failed to put in place proper oversight of Operation Sovereign Borders, the government’s counter-people-smuggling regime.