The head of the Anglican Church in Australia, Dr Philip Freier, has welcomed the inclusion of an Aboriginal co-commissioner to oversee the recently announced Royal Commission into juvenile detention in the Northern Territory.

Attorney-General George Brandis announced Mick Gooda, a prominent Indigenous Australian and Aboriginal and Torres Strait Islander Social Justice Commissioner, would be a co-commissioner of the royal commission along with former Queensland Supreme Court judge Margaret White.

The move came after former Northern Territory chief justice Brian Martin resigned from the position only days after he was appointed, saying today that his resignation did not mean he accepted claims he had a conflict of interest due to his previous role as an NT judge but also acknowledging that he would not have had the full confidence of sections of the Indigenous community which would have been central to the royal commission's inquiry.

Dr Freier, the Archbishop of Melbourne, said he commended Mr Martin's to stand down and the appointment of Mr Gooda and Ms White as co-commissioners. He said in a statement that he also commended the speed with which Prime Minister Malcolm Turnbull has announced the royal commission after an ABC Four Corners program last week highlighted the treatment of juveniles in a Darwin detention centre

"Having just visited a remote Arnhem Land community in my role as Primate of the Anglican Church of Australia, I was made aware again of the high incarceration rate among Indigenous youth," he said.

"In the Northern Territory, 97 per cent of youth held in detention are Indigenous, despite Aboriginal and Torres Strait islander people comprising only 17 per cent of the total NT population. This figure continues to rise and is deplorable. Indeed, research from the Australian Institute of Health and Welfare reveals that children who are placed in detention are three times more likely to return to detention within 12 months of being released."

Dr Freier said Aboriginal Anglicans had told him how important it is for crime prevention and rehabilitation programs to be developed in consultation with Aboriginal people, and also urged the end of mandatory sentencing in the territory.