Three women working on a joint justice project walked out of Police National Headquarters and refused to return because of Wally Haumaha's alleged bullying behaviour towards them.

The policy analysts - two from the Justice Ministry, one from Corrections - were based at PNHQ in Wellington working in the Māori, Pacific, Ethnic Services division run by Haumaha, a superintendent at the time.

They were excited to be working on the cross-sector project, which started in October 2015, to improve "justice outcomes" for Māori, who are over-represented in arrest statistics and the prison population.

A number of alleged verbal bullying incidents, including a particularly heated exchange in which one of Haumaha's senior staff intervened, contributed to the three women leaving PNHQ in June 2016 feeling "devalued and disillusioned".

The three women told their managers, did not return to PNHQ, and continued working on the project from the Justice Ministry offices.

Haumaha, through the police media team, did not respond to a request for comment before deadline.

One of the women said: "Haumaha gave little support and value to the work being done by us and instead belittled our efforts publicly on several occasions."

However, she said she was never asked to make a formal complaint.

The police said concerns were raised but these related to "deliverables and project progress", not bullying allegations.

However, the police have confirmed an allegation of bullying was later made by a third party, although no individuals were named.

On behalf of police, Deputy Commissioner Mike Clement "immediately" contacted the Justice Ministry and Corrections to request more information and advise that the staff involved could make a complaint if they wished.

"No further information or complaints were forthcoming to Mr Clement from the agencies," a police spokeswoman said.

"In the absence of any formal complaint, or further information, the matter was unable to be taken further and therefore not escalated to the Commissioner."

"Police take allegations of bullying seriously. However substantiated information is required about allegations before any follow up actions can be progressed, particularly when the only information available is from a third party not directly involved."

The woman, who spoke on the condition of anonymity, said no one told her Clement had been in touch with Justice or Corrections.

"Nobody told me about it. I'm like, wow, because we would have met with [Clement]," she said, when the Herald told her of the response from police.

"I will make a complaint now. We trusted management to deal with it and never heard back."

She told the Herald the experience was "pretty bruising" and she was extremely disappointed to see Haumaha promoted to deputy commissioner this year.

The process which led to Haumaha's appointment is now the subject of a Government inquiry after the Herald revealed controversial comments he made during a 2004 investigation of police rape allegations against his friends.

"I take responsibility for those comments, I deeply regret them, and I unreservedly apologise for the hurt and concern they have caused. That does not reflect my view or the values I bring to the job every day," Haumaha said.

"My previous association with those individuals does not reflect who I am now nor what the New Zealand Police stands for today."

The woman who was working on the justice project said that problems arose with Haumaha as the team began to question his "police-centric" approach.

"His particular behaviour at such a senior level as one of the managers on the team was quite disturbing to myself and others.

"We were housed in police headquarters but it wasn't only a police project, it was a joint project to improve outcomes for Maori across the justice sector.

"Our team worked holistically and considered the impact on the whole sector, and when we raised issues with Haumaha about his police-centric views, we were brushed off and pretty much told 'you're in my building, do as I say'."

While the police staff followed Haumaha's orders without question, the team from Justice and Corrections would challenge him.

"We were fully supported by our own managers who advocated on our behalf when the working situation with Haumaha continued to deteriorate".

The woman relayed a particular incident, which was overheard by other police and employees on the floor, whereby she and Haumaha had a heated argument where her job was allegedly threatened.

This ended only when one of Haumaha's senior police staff intervened.

"Soon after this incident in a meeting with all the project team and police personnel, the team was basically told that if we weren't with him we were against him and should stand down from the project".

"That was the final straw."

The team left PNHQ and were supported by their respective bosses at the Ministry of Justice and Corrections Services to continue working on the project within the Ministry of Justice.

A senior manager at the Justice Ministry confirmed "issues were raised about the management of the project" in June 2016.

"Some Ministry and Police executives were advised of these issues," deputy chief executive Colin Lynch said in a statement.

"Subsequently, the Ministry decided the Justice employees would work on the project from the Ministry's National Office. The Ministry will not be making any further comment on this matter."

A Corrections spokeswoman said two staff worked on the joint project.

"One of the staff initially worked at Police National Headquarters, and later worked from the Ministry of Justice, which we supported. We are not aware of either staff member making any allegation of bullying."

One of the three women told the Herald they were never asked to provide an official complaint, as they believed their managers would handle it on their behalf.

She said the alleged behaviour of Haumaha raised more questions about his promotion to deputy commissioner.

"Our team knew the importance of this work and what a difference it could make to Maori outcomes. We didn't want to leave, but we had no other choice.

"It's not about the project, it's about the person managing the project."

The Government inquiry into Haumaha's appointment was announced after the Heraldrevealed comments he made during Operation Austin, an investigation into historic police rape allegations made by Louise Nicholas.

He described his friends Brad Shipton as a "softie" and Bob Schollum as a "legend" with women, while one officer told the 2004 investigation into the police sex allegations that Haumaha described Nicholas' allegations as "a nonsense".

While Haumaha has apologised, the Police Minister Stuart Nash said he was unaware of the "deeply disappointing" comments when he gave Haumaha's name to Prime Minister Jacinda Ardern for the deputy commissioner role.

Haumaha was one of two names put forward by the State Services Commission following a recruitment process.

Because of the pending inquiry, Nash has refused to confirm whether Haumaha was the top-ranked candidate.

Police Commissioner Mike Bush was on the panel and has come under pressure since the Herald revealed Deputy Commissioner Mike Clement warned him about promotingHaumaha.

The inquiry was last week thrown into turmoil when the chairwoman Pauline Kingi quit before she started, following a Herald story about her endorsements of Haumaha on a professional networking website. A new chair is expected to be announced this week.

Haumaha's links to New Zealand First have also dogged the inquiry - overseen by Internal Affairs Minister Tracey Martin, a NZ First MP - although the Prime Minister Jacinda Ardern has downplayed any suggestions of a conflict of interest.