The documents allege abuse not only by prisoners, but prison guards as well. The Correctional Service Of Canada won't comment on the allegations, but says complaints are dealt with.
"We've received complaints including sexual assaults, harassment and also complaints about access to medical treatment," said Correctional Investigator of Canada Howard Sapers, The office is an independent body that investigates complaints within the correctional system.
At times, Sapers says transgender inmates are placed in solitary confinement for their protection. However, he is concerned about the overuse of segregation.
"We find that the Correctional Service is relying on segregation as a population management tool," he said.
Change is needed
Jack Saddleback, a transgender activist, said more needs to be done to protect transgender people, who he says are vulnerable.
"It's just horrible to think that trans people are put as second class citizens," he said. "It's a reflection of how much more education we need regarding gender identity, regarding gender expression and regarding cultural sensitivity."
Kyle Kirkup, a researcher at the University of Toronto Faculty of Law says the government needs to update its policies for transgender prisoners. He says transgender inmates would appear before a recognized psychiatric expert to be assessed.
"Transgender people should be allowed to self identify their gender for legal purposes," he said. "So, a person would be asked at admission phase whether or not they would prefer to be place in a men's facility or a women's facility."