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 girl, who is now 3 years old, and one of her siblings were removed from their mother's care by the Department of Child Protection South Australia on April 5.
Fifty-two child protection notifications relating to the child or her siblings were documented between 2002 and 2018, according to the report.
Police "had also conducted investigations in relation to sexual and physical abuse upon her siblings" prior to the alleged sexual assault.
"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 read.
"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].
"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 NT had gone through two major child protection reports, the royal commission into youth detention and child protection and the federal intervention.
One of the notifications — received just four months before the alleged rape — related to one of the girl's sisters and alleged a man aged between 40 and 50 was "buying young girls clothes and taking them to a hotel room".
"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 its response to Ms Gwynne's report, Territory Families wrote it "refutes the finding that 'it was foreseeable that (the girl) was at risk of sexual assault'".
In a shocking admission, Territory Families claimed the risk faced by the little girl before the alleged rape was "not dissimilar" to many other open child protection investigations.
If the approach suggested in the report was used that would result in more kids being taken from their families, it said.
In February, Territory Families reported "no specific concerns that came to Territory Families about particular harm to this child of a sexual nature".
The 25-year-old man charged today over the alleged assault has been remanded in custody to face court on July 26.
"Sex Crime Detectives are carrying out an ongoing investigation into the incident," an NT Police statement read
