A report into the alleged rape of a two-year-old girl in the Northern Territory town of Tennant Creek has found harm was a foreseeable risk that could have been managed or mitigated.

The NT Children's Commissioner report found there had been 35 domestic violence incidents recorded against the parents, including eight aggravated assault convictions for one of them, and more than 150 recorded interactions with police.

The toddler and her four siblings had been the subject of 16 years' of investigations into physical and sexual abuse and neglect, in the lead up to the alleged rape.

The two-year-old girl and one of her siblings were removed from their mother's care by the Department of Child Protection South Australia on April 5.

A 24-year-old man was charged with sexual assault.

Recommendations: Territory Families Undertake an audit of the outcomes of notifications by 30 November, 2018

Undertake an audit of the outcomes of notifications by 30 November, 2018 Ensure that Central Intake is adequately resourced to accommodate peak periods

Ensure that Central Intake is adequately resourced to accommodate peak periods Develop a strategy to address the backlog of overdue investigations

Develop a strategy to address the backlog of overdue investigations Rectify data-recording processes so that notifications are documented separately

Rectify data-recording processes so that notifications are documented separately Adopt a consistent definition of cumulative harm

Adopt a consistent definition of cumulative harm Develop a quality assurance framework to establish a review of child protection policy and practice

Develop a quality assurance framework to establish a review of child protection policy and practice Finalise and implement the framework as a priority Northern Territory Police Establish robust policies and procedures to ensure police comply with the Care and Protection of Children Act

Establish robust policies and procedures to ensure police comply with the Care and Protection of Children Act Review the Child Abuse Taskforce (CAT) mandate to ensure current practice aligns with operational objectives Northern Territory Government Review the achievements of the Children and Families Standing Committee

Review the achievements of the Children and Families Standing Committee Ensure the recommendations of the productivity study of NT child services expenditure are implemented as a priority

Ensure the recommendations of the productivity study of NT child services expenditure are implemented as a priority Review the objectives of the Family Safety Framework and its operation across the NT

Review the objectives of the Family Safety Framework and its operation across the NT Establish a framework for professionals across a range of agencies to share information about children

The toddler suffered "significant and painful" injuries during the alleged sexual assault on February 15 and required a blood transfusion, the independent report tabled in Parliament on Wednesday night found.

"This was not the only violence C1 [the child] had been exposed to, and experienced, in her short life," the document stated.

Fifty-two child protection notifications relating to the child or her siblings were documented between 2002 and 2018, the report noted, and prior to the alleged sexual assault, police "had also conducted investigations in relation to sexual and physical abuse upon her siblings".

"Prior to the birth of C1 [the child], Territory Families had available to it an abundance of evidence relating to the substantial neglect and numerous harms suffered by all of her older siblings," the report noted.

"This included the fact that they themselves sought safety and regularly self-placed with different extended family to avoid return to the care of P1 [a parent]."

The reported stated: "All possible harm types have been identified for these children", including exposure to domestic violence and parental substance abuse, lack of education, neglect, emotional harm, physical harm and sexual abuse.

During the time 52 child protection notifications had been recorded, the Northern Territory had gone through two major child protection reports, the royal commission into youth detention and child protection and the federal intervention.

"This investigation has identified that agencies and service providers continue to work in silos to the detriment of the safety and wellbeing of children," the report said.

In February, Territory Families reported "no specific concerns that came to Territory Families about particular harm to this child of a sexual nature".

System failures led to 'inevitable trauma'

The Children's Commissioner review found children protection services "failed" the girl and there were "critical intervention points" where the system failed the child and her siblings.

"This appears to be a result of inadequate and ad-hoc provision of services and support, the failure to appropriately assess cumulative harm, a culture of reporting and referrals with no or limited evidence of meaningful actions or outcomes," the report stated.

"Interventions were not commensurate to the significant needs of the children based on the level of trauma experienced."

It concluded that if the system failures that led to the "tragic and inevitable trauma" experienced by the child were not addressed urgently, "it is likely that other children will be subjected to, and suffer from, similar traumatic experiences which will continue to affect them throughout their lives."

The report made 14 recommendations specific to Territory Families, NT Police and the Northern Territory Government, including the development of a strategy to address the current backlog of overdue investigations, and an ongoing review of child protection policy and practice.

Territory Families 'missed warning signs and ignored risks'

The case thrust the Northern Territory's handling of child protection cases into the national spotlight.

In March, an internal review undertaken by the Northern Territory Government also concluded child protection services lacked oversight and coordination in its handling of the case.

In response to the Children's Commissioner's report, Territory Families Minister Dale Wakefield conceded reform was needed.

"This report outlines an awful history of unsound decisions and failures to observe policies and procedures by Northern Territory child protection agencies over a 16-year period up until early 2016," she said.

"From 2011 to the end of 2016, there were many points at which the relevant agency missed warning signs and ignored risks.

Ms Wakefield said the Government had accepted the report's recommendations. ( ABC News: Mitchell Woolnough )

"The interests of children were not front and foremost of the deliberations of staff."

Ms Wakefield said the Government had accepted all 14 recommendations, and that work was underway to overhaul the sector, including a $66.9 million pledge to develop a new platform to manage child protection cases, a "thorough review" of the concerns for the wellbeing of children in care policy, and the development of a quality assurance framework for out-of-home care.

Territory Families also accepted the report's recommendations, but proposed the conclusion be amended because "there was not sufficient evidence before the commissioner to draw this finding".

The report said the Children's Commissioner originally found "it was foreseeable that C1 [the child] was at risk of sexual assault and that risk could have been managed or mitigated".

But Territory Families refuted the finding and it was amended in the final report to "it was foreseeable that C1 was at risk of harm and that risk could have been managed or mitigated".

In a response to the Children's Commissioner, NT Police said it would meet with Territory Families to ensure that the policy, procedure and tools used related to notifications and investigations were "appropriate and rigorous".