Two women have now made formal complaints to police about alleged bullying by Deputy Commissioner Wally Haumaha.
The complaints have been sent to the Independent Police Conduct Authority which could also investigate the allegations.
"The IPCA is assessing these matters and will communicate about next steps in due course," Deputy Commissioner Andrew Coster said in a statement.
IPCA general manager Warren Young has now confirmed to the Herald the police watchdog will independently investigate the bullying claims.
The complaints were laid by two of the three women who walked out of Police National Headquarters in June 2016 and refused to return because of Haumaha's alleged behaviour.
The policy analysts - two from the Ministry of Justice, 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.
A number of alleged verbal incidents, including a particularly heated exchange in which one of Haumaha's senior staff allegedly intervened, contributed to the three women feeling "devalued and disillusioned".
The Herald revealed last month that the three women told their managers, did not return to PNHQ, and continued working on the project from the Ministry of Justice offices.
The official confirmation of the two complaints came today after the Herald reported one of the women had laid a formal complaint last week.
Any investigation, either internally by police or the IPCA, will interview other police staff they worked with including one senior police officer, who allegedly intervened in one of the verbal incidents.
Haumaha allegedly called the officer seeking his support several days before the Herald first published the bullying allegations.
The officer reported the conversation with Haumaha to his district commander who in turn alerted senior leadership in Police National Headquarters.
"This will be investigated and we are currently seeking further information about what has occurred to determine what steps are required," Police Commissioner Mike Bush said at the time.
"The Police Executive, including Deputy Commissioner Haumaha, recognise the need to ensure that there is an appropriate level of independence to any investigation of all the matters raised in the media recently, including this most recent allegation."
The two formal complaints come just days after Mary Scholtens, QC, confirmed she would consider the bullying allegations as part of her inquiry into appointment process which led to Haumaha's promotion as the deputy police commissioner.
The inquiry will not look into Haumaha's suitability for the role, rather whether all the relevant information was provided to, or gathered by, the State Services Commission panel which recommended Haumaha as one of two potential candidates for the senior job.
Acting Prime Minister Winston Peters announced the inquiry in June after the Herald revealed controversial comments made by Haumaha about the rape allegations against his friends by Louise Nicholas.
But National MP Chris Bishop wrote to State Services Commissioner Peter Hughes asking for a separate investigation into how the bullying allegations were handled after the three policy analysts left PNHQ.
Three different statements were issued by the Justice Ministry, Corrections and the police, so Bishop wrote to Hughes asking him to clear up the conflicting stories from the three government agencies.
Hughes said he would postpone any decision to conduct his own investigation until after Scholtens' inquiry was complete.
Many of New Zealand's most senior police officers including Commissioner Mike Bush and three of his deputies - Haumaha, Mike Clement and Audrey Sonerson - are likely to be questioned by the QC.
Haumaha was promoted to assistant commissioner in June 2017 by Bush, who was also on the SSC panel which recommended him in May as one of two candidates for the vacant deputy job.
The inquiry into Haumaha's appointment was announced the day the Herald revealed 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, Police Minister Stuart Nash said he was unaware of the "deeply disappointing" comments when he gave Haumaha's name to the Prime Minister for the deputy commissioner role.