Kumanjayi Little Baby, a name used in line with cultural tradition after her death, was reported missing from a home at a town camp on the outskirts of Alice Springs on April 25.
Her disappearance triggered a massive five-day land and air search until her body was found on April 30.
Jefferson Lewis, 47, has been charged with her murder and other offences.
A spokeswoman for Northern Territory Child Protection Minister Robyn Cahill confirmed to AAP that three child protection workers had been stood down on Wednesday morning.
"They've been stood down while an investigation is underway into actions taken, or not taken, in relation to this case," she said.
The minister earlier told news.com.au she had asked her department about the girl's case and had been told there was "nothing to see here".
But when she asked for a briefing she learned there had been about six recent reports made about the girl's living conditions.
The reports related to concerns the girl was living in a Âdangerous environment, was subject to neglect, and was exposed to domestic violence.
"There is an absolute reluctance to move children from Aboriginal families for fear of being accused of creating another stolen generation," the minister said.
"You cannot use that as an excuse if they are not safe."
She flagged a full investigation and called on the NT children's commissioner to run an independent investigation.
