A two-year-old girl was allegedly raped less than two weeks after a man sustained fatal injures at the same Tennant Creek household.
Detectives said the man was allegedly assaulted following a dispute involving a number of people on February 6.
Three days later, the 44-year-old man was taken to the Royal Adelaide Hospital. He died from his injuries last Friday.
Police did not notify Territory Families about the incident on February 6, when the man was allegedly assaulted.
However, according to police, there were 20 notifications from NT police since July 2015 relating to separate incidents about the family of the child, and 16 of those were made directly to Territory Families.
Territory Families has confirmed the department received 21 notifications dating back to August 2015, but only six had been substantiated.
It said the reports did not highlight "specific concerns" about potential harm of a sexual nature to the child, and were "not substantial enough" to remove her from the care of her mother.
The latest incident is just one of 714 cases related to allegations of sexual offences involving children under the age of 16 during the past five years in the Northern Territory, police have revealed.
Already there have been 10 this year.
The cases include a range of sexual offences, including indecent dealings, indecent assaults, sexual relations between minors, some child abuse material matters, as well as historical offences.
Opposition Leader Gary Higgins said Territory Families should not be investigating itself, and is pushing for the Children's Commissioner to review the processes that allowed the child to remain in the household.
NT Children's Commissioner Colleen Gwynne has already launched her own investigation into the incident, and on Wednesday flagged concerns the NT did not have a "proper response" in dealing with "systemic" child sex abuse.
Radio Darwin, Northern Territory Attorney-General Natasha Fyles said alcohol was fuelling "too many of these horrendous crimes" across the territory.