Three child protection workers have been stood down, pending an investigation, over their handling of the case of a five-year-old girl allegedly murdered in Alice Springs as the children’s commissioner faces more calls to investigate.

NT Minister for Children and Families Robyn Cahill is “outraged” at how her child protection department handled the case of the little girl, now referred to as Kumanjayi Little Baby, who disappeared from a town camp on April 25.

Her disappearance sparked a major land and air search before her body was found five days later in the dry Todd River bed.

On Wednesday, Ms Cahill revealed she asked her department for information about its interactions with the girl and her family the day after the child was reported missing. She was advised there were not “any significant concerns”.

Late last Friday, she was told that original advice was wrong, and the department had in fact received child protection notifications about the little girl.

“And as a result of that, I directed an investigation to see how could this be the case and how could this happen?” she told a Darwin radio station.

“That investigation is underway and as of today, three people have been stood down in response to the findings of the investigation so far.”

The investigation relates to actions taken, or not taken, in relation to this case.

“I’m publicly outraged. I cannot get my head around how this sort of situation occurs,” Minister Cahill told 360 with Katie Woolf.

“I can’t express just how angry I am that work that we’ve been doing over the last few months, where I have absolutely said, ‘above all else, the safety of children is what counts most’, has not gotten through to those people on the ground.

“I’m also instigating an investigation of the departmental structure as a whole.”

Ms Cahill said she was “incredibly concerned” about the Aboriginal Child Placement Principle, in which Indigenous children who are removed from their parents are only placed with non-Indigenous carers as an absolute last resort.

She said there was an “absolute reluctance” to remove children from Aboriginal families for fear of being accused of creating another stolen generation.

“You have to get kids … into an environment where we know that the harm can be stopped and then go back and work with the family,” she said.

“The absolute focus should be getting that family into a functional environment that’s safe and that’s the place where you want to see children raised.

“But if it’s not possible, then we have to be realistic about this. We cannot abandon these kids. And quite frankly, that is what we have done.”

The minister said she has “experienced significant pushback” from people, both within and outside of her department, and had been called “racist”.

“People being too afraid to call it out because they’re scared of being accused of creating another stolen generation is absolute rubbish,” she said.

“And we absolutely should be looking at the safety and well-being of these children.

“Take a look at that little girl’s picture and tell me that you don’t think she deserved to be safe.”

Ms Cahill said it “defies logic” that the NT’s current child protection legislation does not mention child safety.

“I absolutely appreciate that sometimes parents find themselves in really difficult situations, and we will do everything we can to help the family as a whole,” she said.

“But at the end of the day, if we can’t guarantee the safety of a child, it is absolutely paramount that we put that child somewhere safe, and then we do the work with the family to see if we can rectify the situation.”

The minister’s comments follow revelations there had been repeated warnings to child protection authorities before Kumanjayi Little Baby vanished from Old Timers Camp on Anzac Day.

According to The Australian, the little girl was the subject of six child protection reports in the six weeks before her death, including one made by police just days before she disappeared.

Police reportedly notified child protection authorities of their concerns on April 22 after responding to an alleged assault on the girl’s mother.

Police, domestic violence workers and relatives had all allegedly raised the alarm about the girl’s exposure to domestic violence and her “dangerous environment”. They also raised concerns about neglect, lack of supervision and unsafe living conditions.

There had been at least 12 child protection notifications about the child, according to the newspaper.

Ms Cahill called on the NT Children’s Commissioner to conduct an independent investigation.

But Children’s Commissioner Shahleena Musk is refusing to investigate Kumanjayi Little Baby’s case, saying she will leave that to the coroner.

“These mechanisms are most appropriately placed to investigate and review the circumstances of this matter and potential contributing and systemic factors,” her spokesperson said on Tuesday.

Jefferson Lewis has been charged with murdering Kumanjayi Little Baby and other offences which cannot be published for legal reasons. The 47-year-old is in custody in Darwin. His case is scheduled for a second mention in the Alice Springs local court on July 30.