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She said a preliminary investigation report found the searches were not covered by the Corrections Act.
She said it was believed a total of 34 women had been subject to "suspected or confirmed internal searches".
"Records reviewed during the investigation were incomplete and of a poor standard, however, they indicated that 38 of the total 42 suspected or confirmed searches that took place were completed by two female doctors, three were carried out by a male doctor and one was carried out by a Corrections nurse."
Leota said there was a current draft investigation report from the Corrections Inspectorate which had found the searches were in breach of policy and procedures.
It had also found the practice was in place at Auckland Regional Women's Corrections between 2006 and 2016.
"There was no evidence found of the practice being systemic at any other prison, however, two isolated confirmed incidents took place within a short period of time in 2016 at Arohata Prison."
So far, 18 women had been contacted, of whom 15 had been paid compensation, received an apology and had been offered counselling. Of the 18, two women said they had not been subject to a search. Discussions with another woman over compensation was under way.
Leota said a further complaint by a prisoner had been made in August 2016 which had been settled the following year, along with an apology.
"We are actively working to contact a further 14 women. These women have previously spent time in prison and are now in the community, and we are working to obtain their current contact information.
"In addition, we are aware that another woman has passed away since she was in prison, and contact will be made with her family."
Leota said it was "critical" Corrections put right the distress the women had suffered.
"These searches were intrusive and potentially traumatising for these women."
She said two doctors who had worked for the prison had their contracts "terminated" in January 2018. One had been partially suspended in October 2016 and both were fully suspended in April 2017.
"The doctor who conducted the two searches at Arohata Prison is no longer contracted to provide services to the Department."
The investigation report had been provided to police and the Medical Council and there was also potential employment action against Corrections staff.
"In addition, legal proceedings are being taken against Corrections by one of the doctors in relation to the suspension and termination of services."
Leota said the prisoners were searched as they were believed to have been carrying contraband internally.
"Women were given the choice of an internal search by a doctor [or] nurse to prove that they were not internally concealing contraband, allowing them to return to their unit more quickly."
She said the issue was first raised in July 2013 by a prisoner who asked to see a prison's inspector. The inspector wrongly told the woman the search was permitted.
The same woman made a complaint in August 2016 which led to the doctor being stood down from the women's prison and the investigation being undertaken.
Sue Gray and Emma Priest, Barristers at Blackstone Chambers in Auckland, said they were acting for one of the women.
They confirmed that had been instructed to give advice on civil proceedings for breaches of the woman's rights under the NZ Bill of Rights Act 1990, which prohibits torture or cruel and degreading treatment.
"Our client confirms that she was detained in the round room, with her only way out being to agree to an invasive internal search," Priest said.
"This search was clearly illegal, abhorrent and constitutes the offence of sexual violation under the Crimes Act.
"The offer from the Department of Corrections specifically allows for legal proceedings despite the payment of compensation."
Amanda Hill, a partner at Cooper Legal, said the compensation was "definitely not enough" and urged the women to seek legal advice before accepting any compensation.
"If they have accepted the offer, I understand it may not be final, so they should seek legal advice anyway," Hill said.
"We are very shocked at this, but sadly not very surprised. Prisoners are extremely vulnerable and that this went on so long, undetected, really reflects the power imbalance in prisons, particularly for women prisoners."
Hill said internal searches often took place in situations where a prisoner was in a "dry cell" - a room without running water or toilet or any ability to wash, and an internal search was "often the only way out".
Tracey McIntosh, University of Auckland's Professor of Indigenous Studies, who was present when some of the women were interviewed, said the searches were "abhorrent".
"They were wrongfully done and illegal under the Act," she said.
"We've had long-time concerns, particularly among women's prisons on the role of searches."
McIntosh said she could attest however, the apology was "truly and sincerely given" and "it was received in kind".
Corrections Minister Kelvin Davis said his department had to ensure it "put it right" and made sure such a practice never happened again.
"This will have been distressing for the women involved. It's not good enough, I'm not happy about it and very concerned that this was ever allowed to happen."
A police spokeswoman said police are aware of the matter and will consider the inspectorate's final report when it is received.
The freephone number for those concerned they were improperly searched is 0800 604 304.
