Minors were arrested and detained in police cells at least 2030 times in 2020/21, based on figures released by the state's Commissioner for Children and Young People Helen Connolly.
Of those almost 890, or about 44 per cent, were Aboriginal while in some regional and remote locations almost all the children arrested were Indigenous.
Ms Connolly's report found that alleged offenders were being held in custody ahead of court appearances or while waiting to be released on bail.
It noted that conflicted with declarations from the United Nations Committee on the Rights of the Child that young people should only be detained for the shortest possible time, separately from adults, and only as a last resort.
The commissioner's findings on youth justice were included in a suite of reports detailing South Australia's progress toward meeting UN recommendations related to a range of issues affecting the state's 369,400 children, including health, education, child protection, youth justice and disability.
"Although some progress has been made, South Australia's state government agencies must continue to work to address the issues outlined in these reports," Ms Connolly said.
"There does appear to be greater awareness in relation to what needs to be done.
"But there is still a reluctance to take actions and make changes at the systemic level which will improve the quality of South Australian children and young people's lives."
Ms Connolly said most disappointing was the limited changes in key areas including the number of children being excluded from school, particularly children living with a disability and those with complex needs and the shortfall in resources to treat growing numbers of young people who required mental health support services.
That pointed to a need for much earlier intervention.
The commissioner also found an inconsistency in the quality and timing of sexual health education, particularly in relation to LGBTQIA+ children, and said there was a need to monitor and address the long-term health, economic and social impacts of the COVID-19 pandemic on young people.
In relation to child protection, her report revealed 80,175 notifications to the Child Abuse Report Line in 2021, down slightly from those in 2020.
It said 4647 children were in some kind of care, including 604 in residential care, also a small decrease.
But it said the number of notifications and the number of children in care remained a concern, noting the five-year trend was still increasing.
Ms Connolly said there would come a time when South Australia could say it was meeting all its obligations under the UNCRC.
"But we're not there yet and we have some major work to do particularly in relation to child protection and child health," she said.
Responding to her reports, a number of welfare groups said her findings highlighted the urgent need for a Human Rights Act in SA.
Australian Lawyers for Human Rights chair Natalie Wade said in the absence of such an act the most vulnerable lived without any legislated framework to directly protect their rights and freedoms.
"Human rights must drive the work of our government and its agencies, from the development of laws and policies, through to the daily decision-making by government that directly impacts our quality of life," Ms Wade said.
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