Indigenous parents struggling with substance abuse are being permanently separated from their children due to delays in Victoria's public health system, a truth-telling inquiry has heard.

Under state law, parents battling problems such as addiction are given up to two years to get the help they need before their children can be permanently placed in out-of-home care.

But it often takes longer to access public mental health, drug and alcohol services, putting Aboriginal and Torres Strait Islander parents at risk of losing their children, the Yoorrook Justice Commission heard.

"The current alcohol and other drug service system is under very significant strain at the moment," Katherine Whetton, deputy secretary, mental health and wellbeing at the Department of Health told the commission on Monday.

"I believe there are waiting lists for those services ... I would say that there would be people that have trouble getting the care and treatment they need."

Aboriginal and Torres Strait Islander children are vastly over-represented in Victoria's child protection system.

They make up more than 20 per cent of children in the system, up from 14.6 per cent in 2016.

Yoorrook is the first formal truth-telling inquiry into past and ongoing injustices against First Nations people in Victoria.

Victorian government ministers, senior bureaucrats and the chief commissioner of Victoria Police are among the witnesses set to give evidence during public hearings examining the impact of injustice within the criminal and child protection systems.

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