Serious accusations of sexual contact between instructors and recruits at NZ Defence Force's Waiouru training centre have emerged.

The office of Defence Minister Ron Mark has confirmed he has been provided a briefing on issues at The Army Depot, where NZ Army recruits go through basic training.

NZ Defence Force issued a press release saying "two members of the leadership team at The Army Depot at Waiouru have been replaced".

It said others had also been removed from their instructor roles while an investigation into "allegations of inappropriate behaviour" was underway.

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"Military Police and command investigations are taking place into a number of offences and significant shortcomings, including inappropriate conduct, failure to follow standing orders, and failure to follow established procedures.

"The investigations relate to seven personnel from The Army Depot. The two members of the leadership team at The Army Depot are not facing investigation."

Chief of Army Major General Peter Kelly said investigations were underway to ensure proper procedure was followed at the Depot.

"As an army, we hold ourselves to the highest levels of behaviour – well above those to which we are legally bound.

"Where we see performance and behaviours that do not match our expectations, we will act.

"The leadership changes we have made were put in place to move The Army Depot forward in a positive way."

Mark said he met with the chief of Defence Force and chief of Army and he "made it very clear how disappointed we are and that we expect strong action."

"In this day and age with this government I expect the highest standard. This behaviour, this conduct is not going to be tolerated.

"It's unacceptable and by military standards it's actually illegal."

Although the investigation is currently underway, the NZDF statement said "it is anticipated that formal disciplinary proceedings will start in the near term".

It stated no further detail would be provided and no interviews would be given.

The issue will be highly sensitive for the NZ Defence Force, given its "Operation Respect" programme which aimed to stamp out sexual harassment and related issues.

The Herald has been told the investigation into senior command at the Army Depot is related to commanders' knowledge of ongoing sexual pursuit of recruits by some of the instructors at the training base.

The investigation is understood to have questioned the leadership of those who were aware of instructors having had sexual contact with recruits.

The questions emerged after an instance of sexual contact between two instructors and a recruit became known.

There is not believed to have been questions raised around consent, although the ban on sexual contact is in part related to the power imbalance between instructors and the youth of most recruits - generally teenagers or in their early 20s.

A military source said there had been concerns across the defence force about elements of the culture that had developed at the Army Depot.

A spokesman for Mark said there was a briefing on the issue on the minister's desk. He had only been made aware of the issue this morning.

"He has asked for a meeting with senior leaders to discuss the issue."

A 2015 evaluation report by the Ministry of Defence into NZDF's recruit programmes made specific recommendations about recruit safety, including the rewriting of the Defence Force order which prohibits personal relationships.

The recommendation said the Defence Force order which "prohibits close personnel relationships in a training environment" needed to be rewritten "to adequately manage stand alone or intermittent acts of inappropriate behaviour or attempts to conduct such behaviour".

The Ministry of Defence report intro recruit training found "there is no tolerance for harassment, bullying or discrimination in a positive learning environment".

However, an anonymous survey found 3 per cent of recruits reported "sexually inappropriate behaviour or language from instructors".

While noting "zero tolerance", the report stated it was "a very low percentage overall".

"We observed that commanders act quickly to remove any instructors who were suspected of being sexually or physically inappropriate with recruits."