For Aboriginal children the rate was 21.5 per cent compared to 13.5 per cent for non-Aboriginal children.
The stark figures were revealed as Department of Families, Fairness and Housing associate secretary Argiri Alisandratos gave evidence at the Yoorrook Justice Commission on Thursday.
He was asked why pregnant women were not allowed to know details about reports against them before giving birth.
Senior counsel Fiona McLeod pointed to previous evidence that often the very first person those mothers saw after delivery was a child protection officer.
"I'd be extremely concerned if the very first person in a birthing suite is a child protection practitioner, that clearly is far from ideal," Mr Alisandratos replied.
Commissioner Sue-Anne Hunter said she was among many Aboriginal mothers who were worried about unborn notifications.
"The reality of our mothers when they're pregnant (is) thinking these children are going to be removed before they're even born," Ms Hunter said.
"If I'm emotional about this (it's) because it's the truth, you go to hospital and you're so worried about a notification happening. You become pregnant, you don't want to tell anybody.
"It's the truth, it's even my story, that I didn't want to and I worked in the system."
Mr Alisandratos revealed 40 per cent of all child protection reports about Aboriginal children met the threshold to be investigated, compared to 29 per cent for the total population.
Commissioners detailed anecdotal evidence that many prisoners who had children in care did not know where they were and had trouble contacting case workers, which Mr Alisandratos said he would look into as parents were meant to be kept up to date.
The associate secretary finished his evidence by committing the department to engaging further with Aboriginal organisations and communities to improve the current system.
