A naval officer accused of physical abusing a female subordinate informed a military court on Wednesday that his actions were justified by intent to instil discipline and were executed with full consent of the subject sailor.

However, prosecutors led by Flight Lieutenant Steven Whybrow argued before the court that what Lieutenant Commander John Jones had committed, which included spanking the female junior officer, was tantamount to indecent behaviour.

Court records showed that Jones reportedly made the unidentified sailor to lie on his lap while he slapped her bare buttocks, incidents that Whybrow said occurred at least twice and clearly without the consent of the victim.

Such activities, the prosecutors said are nothing but the works of a criminal mind, prompting them to file formal charges against the senior officer.

Prosecutors have filed nine counts of indecent acts without consent, five of assaulting a subordinate, nine of prejudicial behaviour, and one count of attempting to destroy defense force property against Jones.

Whybrow told the Australian Associated Press that majority of the incidents, as shared by the complainant, occurred between February and November last year, at around the same time both served an Australian Navy supply ship.

Evidences gathered against the naval officer, Whybrow revealed, include an audio tape recording purportedly made by the female sailor in November 2010, clearly indicating that Jones actually perpetrated the alleged acts.

"It was more of a test to see how disciplined and compliant you were going to be," Jones as reported by AAP as allegedly saying in the secret recording.

In his defense, the naval officer insisted that his behaviour towards the female sailor was mainly motivated by goals to discipline a member of his staff and any actions he dispensed was allowed and approved by the victim.

Whybrow confirmed that Jones admitted to some of the incidents, which the latter stressed were consensual, but the prosecutor said that her client declared otherwise, leaving the naval officer criminally liable.

This latest incident highlighted the Australian Navy's growing reputation of sexism towards female members of the organisation, with recent events including male cadets filming sex acts with female counterparts and letting male colleagues watch the clips.

A recent review about the navy's culture also underscored the troubling emergence of alcoholism among members of the corps.