NOT SAFE: Hamilton man John Samuels fears his son is in serious danger after being sexually assaulted while on remand at Waikeria Prison.

Police are investigating the alleged rape of a teenager on remand at Waikeria Prison.

And the teen's father says a hit has been ordered on his son because he complained to guards.

The prisoner wrote to the Waikato Times this week about ongoing sexual and physical assaults he has endured in prison.

The teen wrote that he was raped in the night by his cellmate within a week of entering prison earlier last month.

His father, John Samuels, yesterday said he would trade places with his son if he could.

The Hamilton man fears his son, 19, might take his own life if he continues to be abused behind bars, and said he would forsake his freedom to know his son was safe.

"Sometimes I wish I was in there," he said. "If I could, I would."

The Department of Corrections confirmed the sexual assault allegation and that police were investigating.

"The scene of the alleged crime was sealed for forensic analysis by police," a spokeswoman said. "Items of the alleged perpetrator's clothing were also collected. He has been charged with misconduct pending any criminal charges being laid by police."

The alleged victim is on remand awaiting sentencing on theft charges. He has a history of property and vehicle theft, but Samuels said his son had attention deficit hyperactivity disorder (ADHD) and also suspected kleptomania, which compelled him to steal.

"He's a good boy. I want my boy to do his time, but safely. He's not safe in there."

Samuels said his son wrote to him every couple of days from prison, and was becoming increasingly desperate.

"He's got a hit on him now because he went to the guards and narked. In his letter he states that he doesn't know if he's going to make it.

"He's either thinking about contemplating taking his life, or they're going to take it for him."

His son was young, slim and mildly effeminate, making him an ideal target for seasoned inmates.

A former prison guard, who declined to be named, confirmed younger, more vulnerable inmates were targeted.

"When you'd walk them from one unit to another they'd give them a bit of a whistle. Prison officers do their best to prevent it, but basically, if it's going to happen it'll happen."

In seven years working in prison he was only aware of two sexual assaults, but admitted there were probably more cases that guards didn't know about.

Corrections is confident Waikeria staff followed protocol and were taking the incident seriously.

"What we can say is that our staff acted immediately to support the prisoner when he disclosed what had happened. He was seen by health services staff without delay and moved to the at-risk unit to monitor his wellbeing. Staff continue [to] ensure that he is safe."

Male Survivors of Sexual Abuse Trust Waikato manager Mike Holloway said it was difficult for police to investigate behind bars because witnesses would not co-operate for fear of being labelled a nark.