Aboriginal woman alleges she was strip searched in front of male detainees at Alexander Maconochie Centre

The head of Canberra's Aboriginal health service has called for an independent inquiry into racism at the Alexander Maconochie Centre in the wake of the allegations, while the Corrections Minister says he "doesn't support" claims racism is rife within the prison.

The woman, who is a sexual abuse survivor, has a heart condition and suffers from mental health issues, wrote a letter outlining the allegations.

In the letter seen by The Canberra Times, the woman said she became upset when she was told she wasn't able to go to her grandmother's funeral.

She said she was taken to the Crisis Support Unit because of concerns for her "safety and mental health".

"I was placed in a cell where everything can be seen. There are also five to seven men housed in the same unit, who can also see everything that occurs," the letter read.

She alleged while laying on a bed, officers in "full squad gear" tried to forcibly cut-off her clothing to ensure she didn't have anything on her.

The woman alleges this happened in view of five male detainees.

"Here I ask you to remember I am a rape victim, so you can only imagine the horror, the screams, the degrading feeling," she wrote.

Winnunga Nimmityjah Aboriginal Health Service chief executive Julie Tongs was "appalled" when she was made aware of the allegations.

"To do that to anybody is just unbelievable," she said.

Ms Tongs said the fact the woman was on remand made the allegations "more disturbing".

She wrote to Corrections Minister Mick Gentleman and the Human Rights Commission on January 21, calling for "as a matter of urgency, an independent, external inquiry into not just this incident but the existence of and response to systemic and institutional racism, bias and discrimination within the AMC."

Ms Tongs said systemic racism was rife within the centre and that was "common knowledge" among the sector.

Mr Gentleman said the Human Rights Commission has commenced an investigation into the detainee's allegations and ACT Corrective Services would assist the Comission however necessary.

He disagrees with claims racism is rife in the prison and said an internal investigation would be launched into the matter as a result of Ms Tongs' concerns.

"I've heard comments before along those lines. I don't support them. It's something we need to look into of course with any sort of allegation and we will do that," he said.

"I do support the [AMC] staff, I don't know that the culture that's provided the assertion from Ms Tongs is correct, but we are certainly looking into it."

Aboriginal and Torres Strait Islander Affairs Minister Rachel Stephen-Smith said she had already reached out to Ms Tongs after she raised concerns months ago about the experience of Indigenous Australians within AMC.

She indicated the government was comitted to an Indigenous-led review into the experience of First Nations people in the justice system, similar to what was conducted into the child protection system.

"There is systemic racism right across our community and I think it would be naive to think any part of the ACT government is the one place where systemic racism doesn't exist," she said.

The Discrimination Commissioner Karen Toohey cannot comment due to privacy constraints.