Canberra's indigenous children risk becoming part of another ''stolen generation'', the head of Australia's peak Aboriginal childcare body says.

The Secretariat of National Aboriginal and Islander Child Care is demanding answers from the ACT government about large numbers of local indigenous children who have been taken from their families by social services.

Secretariat CEO Frank Hytten said unconscious prejudice and a lack of support for families could be contributing to the large numbers of indigenous children in care across Australia.

The latest report on government services published by the Productivity Commission found that on June 30 last year at least 140 of the 559 children in out-of-home care in Canberra were indigenous.

Sixty-three in every 1000 indigenous children were in out-of-home care in the ACT, a rate second only to that of NSW, the report stated. The rate for non-indigenous Canberra children in out-of-home care was 4.9 per 1000.

Australian Institute of Health and Welfare statistics also show in 2002 indigenous Canberra children were six times more likely than those of non-indigenous backgrounds to be removed from their families. This rose to nearly 13 times by 2012.

On average, indigenous children in Australia were 10 times more likely to be placed in out-of-home care, the institute said.

Mr Hytten said the reasons large numbers of indigenous children were being taken into out-of-home care were complex and without a case-by case-analysis determining whether each removal was justified was impossible.

But he said the ACT government should examine the local situation.

"They need to ask that question, why in God's name is it so high, what's going on? Think of the cost of putting all these kids in out-of-home care; it would be a lot cheaper to actually do some preventative work," he said.

The secretariat said that at the rates at which indigenous children were in out-of-home care across the country, Australia risked having another stolen generation. Its statistics show nearly half of all substantiated notifications to protection authorities about indigenous children in Canberra were for neglect.

''If you look at neglect with any kind of insight, some of the things that are considered neglect by middle-class people are not neglect, they are the result of poverty or slightly different child-rearing practices," Mr Hytten said.

In one interstate case, an Aboriginal child was removed without investigation because a doctor reported the child had lost weight.

"The stolen generation was about a very specific act, which was about removing children because they were black; the lighter the skin the more likely they were to be removed.

''What's happening now is far more likely to be unconscious or subconscious prejudices around poverty and a predisposition to believe Aboriginal people are incompetent and useless and drunk."

Mr Hytten said he would like a fifth of out-of-home care budgets across Australia to be gradually reassigned to fund preventive services. More cultural awareness among child-protection staff, hiring more Aboriginal child-protection workers and more appropriate support and prevention services for struggling families could help reduce the number of indigenous children in out-of-home care, he said.

A Community Services Directorate spokesman said the ACT government was committed to tackling the over-representation of Aboriginal and Torres Strait Islander children in out-of-home care. He said a new strategy would focus on preventive measures, family reunification and independent advice on the needs of such children and young people.

''The ACT government supports families when needs first arise and works in partnership with Aboriginal and Torres Strait Islander and non-government organisations who support families in the community,'' the spokesman said. The directorate had four Aboriginal and Torres Strait Islander staff in front-line child protection work.