A man has been charged with the alleged rape of a two-year-old girl.

The 25-year-old has been charged with sexual intercourse without consent, NT Police confirmed to nine.com.au.

The matter relates to an incident in Tennant Creek on February 15, 2018.

The man has been remanded in custody to face court on July 26, 2018.

Sex Crime Detectives are carrying out an ongoing investigation into the incident.

Earlier this month, a scathing report of child welfare services found the girl was clearly at risk of harm which could have been managed or mitigated.

A 24-year-old man was charged with sexual assault over the February attack in which the toddler suffered significant and painful injuries.

She tested positive for a sexually transmitted disease and was provided with post-exposure HIV medication.

She was transferred from Tennant Creek to Alice Springs and then the Adelaide Women's and Children's Hospital for surgery and a blood transfusion, Children's Commissioner Colleen Gwynne said in a report tabled in the NT Parliament.

The girl remains in South Australia with her brother after being removed from their mother's care.

"This was not the only violence that C1 had been exposed to, and experienced, in her short life," Ms Gwynne said, in a heavily redacted report.

"It was foreseeable that C1 was at risk of harm and that risk could have been managed or mitigated."

The report is damning for Territory Families, the department responsible, which said after the attack it had had no specific concerns about the girl.

"Significant contact with police had also occurred with her siblings and both parents, culminating in over 150 recorded interactions," Ms Gwynne said.

Territory Families has rejected the report, denying there was any more or less evidence than "many cases" across the NT to indicate the two-year-old was at risk of being raped.

The notifications to authorities included experience of and exposure to domestic violence and parental substance abuse, lack of education (school attendance), neglect, emotional harm, physical harm and sexual abuse of the children.

"Prior to the most recent alleged sexual assault upon C1, police had also conducted investigations in relation to sexual and physical abuse upon her siblings, some of these investigations resulted in prosecutions, with the perpetrator incarcerated," Ms Gwynne said.