Two Waiouru army base leaders have been stood down and others removed from instructional duties following allegations of inappropriate behaviour.
It's reported the incidents took place at The Army Depot training centre and are believed to have centred on sexual contact between instructors and recruits.
Military police and command investigators are looking into the conduct of seven personnel from The Army Depot.
The alleged offences include inappropriate conduct, failure to follow standing orders, and failure to follow established procedures.
Chief General Peter Kelly told RadioLIVE Drive that seven people are under investigation and two others have been stood down from their command responsibilities.
"They range from instructors, so NCO - non-commissioned officers, corporals and sergeants, to two majors.
"At The Army Depot, where we are responsible for training all the young men and women that join the New Zealand Defence Force and the New Zealand Army, there is very clear guidelines and the induction training that we conduct around the relationship between instructors and recruits," he said.
"With regards to ongoing investigations it's been alleged that a two instructors have had inappropriate relationships with recruits of a sexual nature, which is what we are investigating."
Chief General Kelly says he is "bitterly disappointed" by the allegations.
"We have worked very hard to address some of the cultural issues around sexual assault and prevention in the New Zealand Army and the New Zealand Defence Force."
Questions were raised about how much leaders knew about instructors' sexual contact with recruits, who are usually aged in their early 20s or teens.
The investigation could be a sensitive subject for the Defence Force due to its programme "Operation Respect", which aimed to stamp out sexual harassment and related issues.
Formal disciplinary proceedings are expected to begin in soon. The Defence Force says no further detail will be released at this stage.
Listen to the full interview with Chief General Peter Kelly above.