The man and woman at the centre of an investigation by the Northern Territory Children's Commissioner Colleen Gwynne are accused of abusing 12 Aboriginal children in their care from 2004 to the present.

The children were supposed to be safe after suffering from neglect or harm in their own communities in what has been described as 16 years of "systematic failures" by NT Government departments.

Among the allegations was a complaint by a 15-year-old girl that the adult male carer had sex with her.

The then NT Government Family and Children Services department - now Territory Families - failed in its legal obligation to report the allegation of sexual harm to the police, Ms Gwynne found.

No complaint to police was found, with poor record-keeping and sharing between agencies identified as a major problem.

The man continued to sleep in the same room as some of the children for years afterwards and "attempted to hide this during the home safety check", Ms Gwynne found.

One of the children described him as "the creepy old f... in the grannie flat with teddies everywhere in his room".

There were numerous claims of physical and emotional abuse, including the carers hitting the children with metal pipes and a hockey stick or kicking them.

The woman was accused of racially abusing the children, calling them "filthy black c---s" and on one occasion when one child's poor hygiene was remarked on by school staff she said in front of the child it was because they were Aboriginal.

The children were exposed to negative messages about their families and Aboriginality and discouraged from contact or cultural knowledge about either.

Despite the long list of concerns over many years, Territory Families re-authorised the pair as foster carers in August last year and two children remain in their care.

The investigation found shortcomings, policy breaches and missed opportunities that resulted "in continued physical and emotional harm of the children in care", Ms Gwynne said.

She made 14 recommendations related to Territory Families and other departments, police and the contractor Life Without Barriers, which provides the carers.

"Our investigation into this case revealed a 16-year history of systematic failures to adequately review the suitability of the carers, conduct quality standard of care checks and thoroughly examine allegations of child abuse within the out of home care setting," Ms Gwynne said.

There had been a major overhaul of the child protection system, including reforming the central intake system, more investments into early intervention and prevention services and transforming the out of home care system, Territory Families Minister Dale Wakefield said.

"We have come a long way since then but we acknowledge that there is much to do."

Australian Associated Press