Corrections have admitted more than 30 women were subjected to inappropriate internal searches for contraband.
The department has formally apologised to 15 women and paid them $25,000 compensation - women who were subjected to unacceptable and unlawful searches, some of them multiple times.
The problem was first raised in 2013, but Corrections failed to act for three more years, and it has now admitted that it was wrong.
"We've fronted up and said we've got this wrong. We've fixed it; we've realigned our policies and made it clear what correct practice has been," National Commissioner, Rachel Leota, said.
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The women were suspected of concealing contraband internally, but in these cases there was no contraband found.
Amanda Hill, a lawyer who represented one of the women involved, said the women felt degraded and violated, saying it was "akin to assault".
"It is akin to an assault, so if you think about how a victim of assault feels, then this is effectively the same thing."
Corrections Minister Kelvin Davis said it would have been "distressing for the women involved", adding that it's "not good enough" and that he's "not happy about it and very concerned that this was ever allowed to happen".
"The important thing now is that Corrections do all they can to put it right."
Leota said the searches were intrusive and potentially traumatising for the women.
"While we can't undo the distress they may have suffered at the time or subsequently, it's critical that we try to put things right."
Corrections were first alerted in July 2013 after a prisoner complained and requested to see an inspector after she was searched. That inspector wrongly told her the search was permitted under Corrections' own policy.
Corrections said that person wasn't dealt with appropriately and that her complaint was not dealt with in an appropriate way.
And it's not just against protocol or policy - it's against the law. The Corrections Act says: "Nothing in this Act authorises or permits the internal examination of any body orifice of any person by any officer."
The alternative given to the women was to be confined in what's called a dry room, with no running water and no toilet - it's all done in a plastic container, until officers are satisfied there's no contraband.
"An internal search was one way to get out of that earlier and the reality is a lot of prisoners don't know what their rights are and where the line is," Hill said.
Out of the 42 searches, 38 were completed by female doctors, three by a male doctor and one by a Corrections nurse.
"What has been the consequence for them? I can't go into those details, there are some legal proceedings currently before the courts on those matters," Hill said.
Newshub contacted both police and the Medical Council to see if any criminal charges had been laid against the medical professionals and to see if they were still practicing, but neither responded in time.