One in six Indigenous children received protection services in the past year, and were seven times more likely to engage with authorities than the broader population.
Almost 50,000 Aboriginal and Torres Strait Islander children received protection during the year - a rate of 164.3 per 1000 kids - according to an Australian Health of Welfare report released on Friday.
Rates among Indigenous children were disproportionately high across all states and territories.
The rate of Indigenous children receiving protection services has climbed from 126.9 to 164.3 per 1000 in the past five years, outpacing the increase among non-Indigenous youths.
The rates of Aboriginal and Torres Strait Islander children who were the subject of a substantiated investigation were consistent with findings from previous years.
The findings come as some of the nation's most prominent Aboriginal leaders call for abused Indigenous children to be removed from their families.
Indigenous leaders say children with sexually-transmitted diseases must be separated from their families, after the rape of a toddler in the Northern Territory and soaring rates of infection laid bare by a royal commission.
The head of the Territory Stolen Generations Aboriginal Corporation Eileen Cummings said programs needed to be put in place to support children and parents.
"Children can't grow up not knowing who their parents are, so I want the Government to try and put in place a program to get the parents back on track so they can't take the responsibility for their children," she told the ABC.
She also said that authorities were hesitant about removing children for fear of backlash.
"I think they are reluctant [to remove children] but maybe there should be an advisory council that can help them make the right decisions, because at the moment they're not making the right decisions," Ms Cummings said.
Former adviser to Prime Minister Malcolm Turnbull on Indigenous Affairs Warren Mundine also said there needed to be action.
“Culture is not a reason to leave a child in an unsafe or neglectful home,” he told The Australian.
“Indigenous children can be raised with their culture and language even in adoptive families. And, frankly, if parents can’t take care of their children’s basic needs, wellbeing and safety, I’d question what culture their children are learning anyway.”
However there are many who have criticised protection services for unnecessary removals and for getting it wrong.
Last year NITV News revealed children taken into out of home care in Queensland had ended up covered in bruises and appeared to have been abused once removed from their families.
The Australian Health of Welfare report was criticised today for failing to include rates of abuse in out of home care, after children were removed from their families,
In a piece written for The Conversation today, academic Katherine Mcfarlane said without this information we were only seeing part of the picture of child abuse.
"There is no reliable national data in this report on the number of notifications, investigations and substantiations of abuse that takes place when a child is in out-of-home care," she wrote.
The Australian Health of Welfare report stated that: "these cases cannot be separately identified in the national data".
According to Mcfarlane though: "Without this basic information on the national rate, government assurances that children are safe in out-of-home care ring hollow."
Why so many Indigenous children?
The institute said the reasons for the over-representation of Indigenous children in protection were complex.
"The legacy of past policies of forced removal, intergenerational effects of previous separations from family and culture, a higher likelihood of living in the lowest socio-economic areas and perceptions arising from cultural differences in child-rearing practices are all underlying causes," the report said.
The institute said drug and alcohol abuse and family violence might also be contributing factors.
"Indigenous children are also over-represented in other areas related to child safety, including hospital admissions for injuries and assault, experiences of homelessness, and involvement in the youth justice system," the report said.
Emotional abuse and neglect were the most common types of substantiated abuse investigations for both Indigenous and non-Indigenous children.
The average age of engagement with child protection services was the same (eight years old) among Indigenous and non-Indigenous youths, but a slightly higher proportion of Indigenous kids were aged under five.
Indigenous children were 10 times more likely to be subjected to "care and protection" orders or in out-of-home care.
Across Australia in the past year, 68 per cent of Indigenous children were placed with relatives or kin, other Indigenous caregivers, or Indigenous residential care, in similar rates to previous years.
Indigenous children from the lowest socio-economic areas were far more likely than non-Indigenous peers from the same areas to be the subject of a substantiated investigation.
The 102-page report laid bare a wide range of findings into trends within child protection.
KEY FINDINGS OF THE CHILD PROTECTION REPORT:
* One in 32 Australian children (168,352) received protection services in 2016-17;
* Indigenous children are seven times more likely than non-Indigenous kids to interact with child protection services;
* The number of children receiving protection has risen by about 25 per cent over five years, with a steeper increase for Indigenous kids;
* $4.3 billion was spent on child protection and out-of-home care in 2016-17, an annual increase of $327 million or 8 per cent;
* 74 per cent of children who received child protection services are repeat clients;
* 32,600 children have been in out-of-home care for two years or more;
* Children from very remote areas are four times as likely as those from major cities to be the subject of a substantiated investigation;
* Children from poorer areas are far more likely to engage with protective services than those from the most affluent areas;
* Girls are slightly more likely to experience sexual abuse than boys, consistent with recorded crime statistics for sexual assault;
* Boys have slightly higher rates of exposure to neglect, physical abuse and emotional abuse; and
* Police were the most likely to notify child protection authorities that investigations ought be carried out, followed closely by school staff. Just 0.3 per cent of notifications came from the child involved.
(Source: Australian Institute of Health and Welfare 'Child Protection Australia 2016-17)