An ACT government schools program, meant to help vulnerable children get a good start, risks creating ''schools of choice'' for middle-class families, according to the Auditor-General Maxine Cooper.

Dr Cooper found that an indigenous pre-school program has a ''disproportionately low'' number of Aboriginal and Torres Strait Islander children enrolled.

While Dr Cooper's office found that the government's Early Childhood Programs were successfully helping more than 1000 Canberra children, the auditor found the schemes need to be better targeted so they could reach the youngsters for whom they were designed.

The Education Directorate's four Early Childhood Schools in Narrabundah, Lyons, Scullin and Isabella Plains were introduced in 2009 with the purpose of improving early learning and development for children, particularly children at risk, and have proved popular with parents.

A fifth Early Childhood School is scheduled to open in Franklin next year.

But Dr Cooper found that education authorities were not targeting disadvantaged children for potential recruitment and could not say how many youngsters from these groups were attending the schools.

''Without a strategy of planning for, and engaging with, socially or economically disadvantaged families, there is a risk that the schools become 'schools of choice' for ACT families, who recognise the benefits of the model and the suite of services that are delivered,'' the Auditor-General wrote.

Dr Cooper also found the Early Childhood Schools were more expensive than their bigger mainstream counterparts with annual cost per student of between $12,800 and $18,700 compared to $9520 to $11,644 per student at larger government primary schools.

Dr Cooper also expressed concern about the territory's five Koori Preschool Programs, which she said provided important services for some Aboriginal and Torres Strait Islander children.

''Generating enrolments in the programs is an issue and there is evidence to indicate that a disproportionately low number of eligible Aboriginal and Torres Strait Islander children are enrolled in the programs,'' she wrote.

''A concerted effort needs to be made to engage with the Aboriginal and Torres Strait Islander community to encourage interest and enrolments in the programs.''

Dr Cooper found there was no clear idea in the bureaucracy of who was responsible or accountable for ensuring the services were being used by the ''target group'', nor were systems in place to identify needy children by other agencies such as Community Services or ACT Health.

Education Minister Chris Bourke welcomed the report yesterday and said he would be considering Dr Cooper's recommendations.

''We are continually working to improve the quality of our early childhood education and targeted programs that are vital to giving children the best start in life,'' Dr Bourke said.

''This report provides valuable advice on how to make our system even better for Canberra families, particularly those that require additional support.''

Opposition education spokesman Steve Dozspot said he would ''be following up to ensure Chris Bourke acts on these concerning findings''.