One boy was five when he had his first child protection report and had many others into his teenage years, but most were closed without investigation.
He also wasn't given counselling after reporting he was a victim of sexual abuse.
The landmark Taskforce 1000 report "Always was, always will be Koori children" reveals the number of Aboriginal children in out-of-home care almost doubled in the past five years.
"The Victorian child protection system is faced with a crisis," the report says.
Commissioner for Aboriginal Children and Young People Andrew Jackomos says children are being taken from home for their own safety only for many to suffer physical, mental and cultural neglect across multiple agencies.
"Many children did not know they were Aboriginal, were split from siblings, and left for years in residential care -isolated from family, culture and country - when they might have been in the loving care of grandparents or other
relatives," Mr Jackomos said on Wednesday.
"We had child protection officials tell us they had been unable to trace a child's Aboriginal family for years when we were able to track them down on Facebook within minutes."
A review of 980 Aboriginal children's cases found 88 per cent of the children had experienced family violence, and 87 per cent were exposed to parental substance abuse.
It recommends improving the child protection services for Aboriginal children and building the cultural competency of protection agencies.
"We know that Aboriginal children do better when they remain connected to their community and to their culture."
Victorian Children's Minister Jenny Mikakos said the government had accepted all the recommendations "in full or in part or on principle".
"The case studies, the findings are very concerning. It's completely unacceptable the significant over representation that we have," Ms Mikakos told reporters.
She said work was already under way to increase the number of Aboriginal staff working in child protection and there was funding to get more Aboriginal foster carers.
"We know that Aboriginal children do better when they remain connected to their community and to their culture," she said.
National domestic violence helpline: 1800 737 732 or 1800RESPECT. In an emergency call triple-zero.