Kumanjayi Little Baby, a name used in line with cultural tradition after her death, was reported missing from a home at Old Timers town camp on the outskirts of Alice Springs on April 25.
Her disappearance triggered a massive land and air search until her body was found five days later.
Jefferson Lewis, 47, has been charged with the five-year-old's murder and other offences.
Northern Territory Child Protection Minister Robyn Cahill confirmed on Wednesday that three child protection workers had been stood down over the girl's case.
She said she had contacted the Department of Children and Families to find out if there were areas of concern regarding the girl.
"I was basically told that things were not a situation of concern," Ms Cahill told reporters in Darwin.
The minister said she then requested a full brief, which indicated the need to investigate how processes had been carried out.
"As a result of the initial investigation that had occurred, there's been three staff that have been stood down from the roles that they were occupying," she said.
"That wasn't my decision, that was a decision of the department."
Ms Cahill said she could not talk about specifics of how the girl came to the department's attention.
There were reportedly six recent reports made by police, women's shelter staff and a relative about the girl's living conditions and her potential exposure to harm.
A broader independent investigation into the structure of the department was needed, the minister said, with a probable restructure down the track.
Child protection in the NT had been under a lot of pressure for a very long time without significant change, Ms Cahill said.
"There are so many children who have had repeated notifications made where zero action is taken for a number of years and those children subsequently have ended up in the criminal justice system," she said.
"We're not going to be able to deliver better outcomes for children unless we shift our focus."
Lewis was arrested at the town camp after he identified himself to residents, who beat him unconscious.
He was placed under guard at Alice Springs Hospital, where an angry crowd demanded he face traditional justice, with some rioters looting local businesses.
Lewis was flown to Darwin by the NT Police air wing to protect him and hospital staff.
Police said 30 people had been arrested in relation to the riots and looting.
The girl's death has spurred calls from the federal opposition for a review of conditions within town camps and money spent on the sites, as well as a royal commission into the abuse of Indigenous children.
National Aboriginal and Torres Strait Islander Legal Services chair Nerita Waight said the girl's death highlighted systemic failures.
"There is a moral imperative for politicians to create laws and policies that stop (these events) from occurring," she said.
"Instead they are encouraging laws that incarcerate people and make communities more dangerous."
A candlelight vigil in honour of Kumanjayi Little Baby will be held in Alice Springs and other places around Australia on Thursday evening, with participants asked to wear pink, her favourite colour.
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