The apology comes after a Herald investigation this morning revealed Haumaha questioned why Louise Nicholas publicly accused his friends in the police of raping her in the 1980s and continued to support them after the scandal broke, according to interviews with fellow officers.
One officer told the 2004 Operation Austin investigation into the police sex allegations that Haumaha – who was appointed to the senior role by Police Minister Stuart Nash last month – described Nicholas' allegations as "a nonsense" and that "nothing really happened and we have to stick together".
This morning, Nash said he was unaware of Haumaha's "deeply disappointing" and "unacceptable" comments before recommending his appointment to the statutory role of deputy commissioner.
Haumaha has declined requests for an interview.
But in a just-released statement, he said acknowledged the "concerns expressed by Louise Nicholas and others" around my comments from 2004 regarding Operation Austin.
"It is important to say outright that 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.
"In the 14 years since those comments, and particularly through the changes following the 2007 Commission of Inquiry, I have reflected deeply and often on what it means to live the values that New Zealanders rightly expect from their police.
"I recently met with Louise to assure her of my commitment to the work the organisation has done as a result of the Commission of Inquiry to improve our culture, and our service to victims of sexual assault.
"My previous association with those individuals does not reflect who I am now nor what the NZ Police stands for today.
"The culture of NZ Police has changed for the better in recent years as a result of the Inquiry and an ongoing commitment to our values, but there is still more work to do.
"My focus is on working tirelessly in NZ Police to build the trust and confidence of our communities."
The apology comes soon after Acting Prime Minister Winston Peters has announced an "investigation" into whether the Government had all the information it needed before promoting Haumaha to deputy police commissioner.
Police National Headquarters are yet to answer what was disclosed to the State Services Commission, which managed the recruitment process.
Commissioner Mike Bush was on the interview panel as the representative of the Minister and last night said Haumaha "deeply regretted" the comments, but was also a highly respected leader who has driven change within the police culture.
Today, State Services Commissioner Peter Hughes declined to comment on what Bush told the recruitment panel.
"It is the Commission's practice to publish the key relevant appointment process papers at the time the appointment is announced. Information relating to individual candidates is not released to protect the privacy of the individuals involved and the integrity of the recruitment process itself."
Since then, Acting Prime Minister Winston Peters waded into the debate and said questions would be asked of the recruitment process.
"We're going to have a full investigation as to the process, as to the adequacy, as to whether we heard all the information we should have heard and ensure the process was properly done," Peters said this afternoon.
"We're not going to rush to judgment until we do find out what happened here."
Advocates for survivors of sexual abuse this morning urged Haumaha to go further than expressing "deep regret" and apologise.
"Those kind of comments have consequences," said Kathryn McPhillips, the executive director of Help Auckland.
"They hurt people. And being regretful is one thing but addressing the harm is also an important step."
Andrea Black, the national head of Rape Crisis, agreed an apology was necessary.
"Regret is not enough. You can regret you said something but a true heartfelt apology for the psychological harm, and potential emotional damage, and perpetrating the rape myths would be outstanding - and would go some way towards proving true change has occurred."
Haumaha was close friends with Clint Rickards, Brad Shipton and Bob Schollum when they worked together at the Rotorua police station in the 1980s and 1990s.
He remained friends with them after they left the station and telephoned Rickards - who was by then the Assistant Commissioner in charge of Auckland - shortly after Nicholas publicly alleged in 2004 the trio raped her in group sex sessions.
Her allegations - including being violated with a police baton -triggered an exhaustive police investigation, Operation Austin, as well as a Commission of Inquiry into the culture of the police and how sexual assault cases were investigated.
Rickards, Shipton and Schollum claimed the group sex with Nicholas was consensual and were found not guilty at the 2006 trial.
The jury was unaware Shipton and Schollum were already in prison on other rape charges laid by Operation Austin.
"Your arrogance, in my view, knew no bounds," Justice Ronald Young told Shipton and Schollum in sending them to prison.
"You were confident you could commit a serious crime and get away with it because you were policemen - and you almost did.''
The investigation also led to a prison sentence for John Dewar, the former head of the Rotorua CIB who was convicted of four charges of attempting to pervert the course of justice.
He covered up the historic sex allegations against Rickards, Shipton and Schollum when Nicholas first came forward in 1993, as well as giving inadmissible evidence at two trials of another police officer Nicholas alleged raped her as a teenager.
Operation Austin and the Commission of Inquiry, led by Dame Margaret Bazley, exposed sleazy elements of police culture and led to widespread changes in the force.
Detectives interviewed colleagues of the trio shortly after an investigation by the Dominion Post and TVNZ published Nicholas' allegations in January 2004.
Haumaha was a senior sergeant in Rotorua when he was interviewed about the culture of the station in the 1980s.
"In a nutshell, the culture of the police in the mid 80s was work hard and play hard in terms of enjoying ourselves," he said to the Operation Austin investigation.
Haumaha told Detective Sergeant John Price, now the superintendent in charge of the Canterbury district, that he was aware Dewar investigated Nicholas' rape complaint in 1993, although he never heard any mention of a police baton.
He described Schollum as a good friend, a dynamic leader and a "legend in his own right".
"It was no secret that Bob was attractive to a lot of women. The legend was that he was never short of a girlfriend or female company," Haumaha told Price.
He also offered the name and phone number of a woman from his marae, whose daughter babysat for Schollum, to vouch for him.
"My people who knew Bob were shocked by these allegations of rape, as this was not the Bob they knew."
Haumaha also spoke highly of Rickards and Shipton, who was an "awesome cop and good friend" whom other police officers were jealous of.
Shipton never mentioned anything about group sex, Nicholas or a baton, Haumaha told Price.
"I feel that people got the wrong impression of Brad. He was a big softie at heart."
Haumaha volunteered to Price that he called Rickards as soon as the Nicholas allegations were published and his friend adamantly denied them.
And, according to the statement of another Rotorua police officer, Haumaha believed the allegations were "nonsense".
Lynton "Knocker" Dean said he met Haumaha in February 2004.
Haumaha, according to Dean's statement, raised the Nicholas allegations and said "how much of a nonsense it was and how could anyone come out and drag it all up".
"He also said something along the lines, you know nothing really happened and we have to stick together," Dean told Detective Sergeant Grant Johnstone.
"I think he was referring to the people that were around at that time."
Speaking last night from his home in Rarotonga, Knocker Dean said: "I stand by my statement 100 per cent".
"Wally was mates with those guys, he put them on a pedestal. I had a number of conversations with him where he defended them," said Dean.
"I've never heard him denounce their behaviour."
Since that time, Haumaha has risen through the ranks and this month replaced Viv Rickard as the deputy commissioner, a statutory role for a five-year period.
Police Minister Stuart Nash lauded his "clear vision and leadership skills".
"I expect him to play a key role to strengthen Māori leadership within Police and enhance the relationship between police and Māori communities, to reduce victimisation and offending."
Nicholas acknowledged what Haumaha has achieved but pointed to his statement to Operation Austin - and other remarks attributed to him by Dean - as evidence of a poor attitude towards women.
"I had seen Wally around in Rotorua. Clearly he ran with this crowd," said Nicholas, referring Haumaha's statement about his friendship with the men she accused of rape.
"I'm not saying he did anything wrong, I don't know. But I've never been comfortable standing in the same room with Wally because he was mates with these guys."
At a chance meeting at a Police College event in the past year or so, Nicholas said she declined an offer from Haumaha to have a "cup of coffee and put water under the bridge".
But when he was appointed to the deputy role, Nicholas said she "hit the roof" and asked for a meeting with Bush and Haumaha.
She also insisted Deputy Commissioner Mike Clement, who was a senior member of the Operation Austin team, be present.
"I didn't hold back. I said 'I've read your statement Wally and I know what you said. You put it out there about how wonderful these men were'," said Nicholas.
She was reluctant about speaking publicly for fear of being branded racist; an attack levelled at her by supporters of Clint Rickards at the time of her original allegations.
"I'm not doing this to be a vindictive bitch. The police have worked hard to change their culture over the last 10 years or so," said Nicholas.
"But without the right leadership, without the right attitude towards women, they can tumble backwards.
"Will Wally uphold what the police have fought hard for? Or will he take the foot off the accelerator?"
Bush confirmed Haumaha met Nicholas to "assure her he remains committed to continuing the work the organisation has done as a result of the Commission of Inquiry to improve our culture and our service to victims of sexual assault".
"He highly values the relationship that NZ Police has with Louise Nicholas.
"He emphasises our values of empathy, diversity at every opportunity both with staff and the public. He has been recognised several times for this work including a QSM and ONZM."