Fifteen prisoners have complained of being sexually assaulted by their cellmates in the past seven years.
The Department of Corrections released the data to RNZ under the Official Information Act, following the sentencing of Stephen Mark Gotty for a sex attack.
Gotty, a repeat sex offender, was allowed to choose his cellmate, and he sexually attacked the 19-year-old once their cell door was locked on their first night.
According to Corrections, 15 prisoners subject to double-bunking have complained of being sexually assaulted by their cellmate, in or outside their cell, from 2010 to 2016.
More than 1200 physical assaults on double-bunking prisoners were reported in prisons around the country over the same period.
Ken Clearwater, who manages the group Male Survivors of Sexual Abuse, said sexual attacks in prison would be under-reported.
"And no one's going to report it because, as you know, narks get beaten up ... it's certainly something we have to look into."
According to a government report, only 9 percent of sexual offending in the general population is ever reported to police.
Mr Clearwater said that figure would be even lower amongst the prison population.
He said double-bunking made the situation even worse.
"I think it's the most dangerous thing you can do in this country, especially when you've got vulnerable people going into that prison system to be double-bunked. I think it's appalling and definitely inhumane."
Mr Clearwater's organisation has helped survivors of rape inside prison.
"We talk to them and say: 'Look, do you want us to go to the police?' And they say: 'Definitely not.'
"The shame and the guilt that goes with it is massive ... Because they're carrying shame and guilt. They don't want anyone to think that they've been raped because that means they've been weak, and they certainly don't want to complain about it within the prison system, because if it gets around that you've narked on somebody then the chances of you getting a beating are pretty high."
Corrections chief custodial officer Neil Beales said authorities could not do anything unless prisoners came forward.
"Of course, in certain circumstances, it does bring risks with that, but it's important for prisoners to be able to rise above that and tell us what's going on so that we can help them.
"Because if they're under threat, then we can help and if something happens as a result of that then we will take the appropriate action against the perpetrator of violence in every incident where we've got the evidence and information to do so."
He said Corrections could place the victim or the perpetrator in a new unit.
Gotty's choice of bunkmate only possible via failed processes
A criminology tutor at Victoria University, Roger Brooking, said Corrections had not been able to explain to him how the repeat sex offender was allowed to choose his cellmate.
He said the teenager was a remand prisoner and should never have been bunked with Gotty.
"If you look at the judge's sentencing report on Gotty he was already in prison for a previous sentence on a 17-year-old.
"So he was a sentenced prisoner and the young feller was a remand prisoner."
He said Corrections' risk assessment of the case was poor.
The department said Gotty was only able to choose his double-bunking partner because SERCO and Corrections staff at Mt Eden failed to follow processes.
Prison staff have had the rules reiterated to them since Gotty's sex attack, but Corrections' Neal Beales said no process could be fault-free.
"These processes are really, really good, and if they're followed to the letter they can take you to a very high-level of assurance and protection, but they cannot ever give you 100 percent assurety that nothing ever will happen, because you've got two human beings inside that cell."
He said violence and sex assaults could take place in corridors, showers and gymnasiums and were not dependent on double-bunking.
"I don't want people to believe that our prisoners are being sexually assaulted every day.
"It's actually far less prevalent than the movies and films would have you believe, and we also know that the vast majority of prisoners in our care are just getting on with their day doing their offending behaviour programmes. They don't want violence in prisons, they don't want to be assaulted, they don't want to assault anybody else."
Gotty is serving a sentence of preventive detention with a minimum non-parole period of nine years, meaning he will have to prove he is no longer a threat to society before he is released.
The prison officers who allowed him to choose his cellmate have faced disciplinary action.
In its response to RNZ's request for information, the department would not say what that involved, citing privacy issues.
RNZ also asked whether any compensation had been paid to the prisoner. The department said it made attempts to meet with and apologise to the man. It was unclear if that had happened.