Military police told a rape complainant she faced a charge of wrongly being in a male barracks room after she told police she was taken there while too drunk to resist and then sexually assaulted.

The threat came after the woman made a complaint to NZ Police, saying she had been raped by an instructor who offered to help her back to her room but instead took her to his quarters.

Police were told by the woman that she did not want to be there, did not want to have sex and was unable to consent.

The incident happened two years ago but the alleged attacker was only stood down from his position this week.

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The case follows the move last month by the NZ Defence Force to tackle "inappropriate behaviour" and questions around command at The Army Depot, the Waiouru base where recruits are sent for basic training.

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It saw two members of The Army Depot's leadership team replaced and five others removed from their duties as instructors because of "a number of offences and significant shortcomings".

The alleged perpetrator in the rape complaint - a non-commissioned officer - was stood down on Thursday as new commanders brought into The Army Depot reviewed previous leadership decisions.

The complainant - who was not a recruit and remains a uniformed member of the defence force - went to police in July 2016 to report she had been raped at Waiouru Military Camp.

The complaint recorded that a drinking session led to the complainant requiring assistance to find her room and how she was escorted by the alleged perpetrator to his room where sexual contact took place.

Police were told she was unable to consent and did not want the sexual contact.

The Weekend Herald has learned the NZ Police inquiry did not find evidence to support a successful prosecution and passed the investigation file to NZ Defence Force military police, which reached the same conclusion.

A November 2017 email seen by the Weekend Herald showed the military police investigator - an RNZAF flight sergeant - told the complainant he was considering offences she had committed under the Armed Forces Discipline Act and The Army Depot "standing orders".

"Standing orders" are the baseline military rules every uniformed soldier is obliged to follow. The Army Depot orders include commands around alcohol use and people not being in the rooms of opposing genders.

The flight sergeant's email, copied to a number of people, said the investigation found potential offences included the fact the alleged perpetrator "had a visitor in his barrack room and that you were out of bounds by being in a male's barracks".

The flight sergeant wrote that the "orders offences implicate both of you".

However, he said he had "decided to recommend that these charges not be pursued" although the final decision was up to the commanding officer.

It is understood no further action was taken.

The alleged perpetrator was a recruit instructor at NZ Defence Force's The Army Depot in Waiouru.

An NZDF spokesman said the decision to remove the alleged perpetrator from his duties came when new commanders reviewed previous leadership decisions and discovered "other disciplinary matters regarding this person warranted further consideration".

Support had been provided to the complainant by the NZDF sexual assault response team, he said.

"It is considered that if the New Zealand Police were unable to lay charges in respect of this allegation, the NZDF would also be unable to."

The spokesman said the decision to stand down the individual - a non-commissioned officer - was made while "other disciplinary matters related to this matter are resolved".

The removal of The Army Depot leadership meant a new command team was reviewing "previous leadership decisions including considering whether any further action can be taken on this matter, outside of the Police investigation".

NZ Police Detective Inspector Steve Wood said a complaint of sexual assault was made on July 30 2016.

Wood said the complainant reported the alleged assault having happened about three weeks earlier at the Waiouru Military Camp.

Police staff in Dunedin and in Central Districts - which includes Waiouru - were involved in the investigation.

"However, due to a lack of evidential sufficiency the investigation was unable to be progressed further. This outcome was explained to the victim."

Wood said support was offered to the victim and military police were told of the inquiry.

Minister of Defence Ron Mark said the case highlighted by the Weekend Herald would be one of those "under investigation", but couldn't comment further as he didn't want to "prejudice any potential charges".

Mark said sexual assault, harassment, bullying and other abusive behaviours had no place in society and particularly in the NZDF.

He said those currently servicing were "part of a wonderful organisation that does incredible things for New Zealand… which is why these types of behaviours cannot be tolerated".

"If you think this type of behaviour is acceptable in this day and age, then get out. You are sullying the legacy of the women and men who have served the NZDF. We do not want you in our defence force."