A senior Navy officer has been stripped of his command, another will be sanctioned and others counselled over their involvement in incursions into Indonesian waters last summer while enforcing the Government's asylum seeker boats policy.

A joint review into the incidents by Customs and Border Protection and the Defence Force, released in part in February, found Australian Navy and Customs ships had entered Indonesian waters six times last December and January.

It found commanders had incorrectly calculated the location of the maritime border during Operation Sovereign Borders (OSB).

The report also recommended that the Chief of Navy consider whether there had been any lapses in professional conduct.

A statement from Defence says the Chief of Navy, Vice Admiral Ray Griggs, has been considering the role of the seven Commanding Officers (COs) involved.

"As a result the Chief of Navy will remove one Commanding Officer from his command and another will be administratively sanctioned. The remaining Commanding Officers will be formally or informally counselled," the statement says.

An administrative sanction is a formal warning that can vary in severity and can affect prospects for promotion.

The Defence statement says the Navy Chief accepts that none of the COs involved "deliberately contravened orders".

"These actions are 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," Vice Admiral Griggs said in the statement.

The Defence statement explains that "in each instance of an incursion there was clear operational direction not to proceed within 12 nautical miles from the Indonesian archipelagic baseline".

It says the Chief of Navy carefully considered the positioning of each ship involved and that each CO was able to put their "perspectives" directly to him.

The action has prompted the federal Opposition to criticise the Government for not putting in place "proper oversight".

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Labor's acting spokesman for Defence David Feeney has cited reports that the Operation Sovereign Borders Joint Agency Taskforce had ordered ships "too close" to Indonesian territorial waters.

"It is 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," Senator Feeney said in a statement.

But the Government has "strongly" rejected the accusation, with a spokesman for Defence Minister David Johnston saying Senator Feeney was yesterday personally briefed by the Navy Chief.

"The Chief of Navy worked through this issue very deliberately and focussed the accountability solely on the issues that were under the control of each of the Commanding Officers," the spokesman said in a statement.

In February, Defence Force Chief David Hurley said the Australian Navy's incursions into Indonesian waters, while enforcing Operation Sovereign Borders, had led to a "go slow" on the military relationship between the two countries.

General Hurley said he could not disclose how far Australian ships went into Indonesian waters but said the personnel involved were not using the "appropriate information".