Winnunga Nimmityjah Aboriginal Health Service says there have been long and unnecessary delays to patients being transferred to its new prison health service.
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The health clinic was a long-awaited government promise to improve the health of Indigenous detainees, which formally started in January.
It allows Indigenous detainees at the Alexander Maconochie Centre to access an Aboriginal-controlled and managed health clinic within the prison.
It was prompted by the death of Steven Freeman at the prison and the report by Phillip Moss into his care.
But six months after its official opening, problems are emerging.
Winnunga chief executive Julie Tongs said the biggest hurdle had been getting clinical handovers from Justice Health.
"We signed off on a memorandum of understanding on December 21 last year and it was agreed that Justice Health would do the handovers within 72 hours," she said.
"Some of those handovers have taken months."
Ms Tongs said she believed many of the issues stemmed from Justice Health being short-staffed.
She said there were also difficulties getting access to medical files, and Winnunga had encountered "territorialism" from other Justice staff.
"I'm not sure what it is about Winnunga that they don't trust," she said.
Ms Tongs said her staff had been unable to access clients' medication charges, which were kept separately to discharge information by Justice Health.
"Previously my staff were able to scan the medication chart because that's one of the most important pieces of information we need to have," she said.
"But they've stopped us from doing that. That's not good enough and it creates a dangerous situation."
She said there were also issues around patient privacy.
"We would never put anyone at risk by not sharing information that was needed. But there is an oversharing of information from Justice Health with corrections staff and that's poor practice," Ms Tongs said.
Liberal MLA Giulia Jones questioned government officials about the health transition at an ACT Estimates hearing.
Canberra Health Services chief executive Bernadette McDonald said she was working in partnership with Winnunga on the issues.
She said a committee met weekly to discuss issues as they arise.
When questioned about not all medical information being transferred over, Ms McDonald said she would follow the issue up.
"As much medical information is provided as possible," she said.