The girl, Sharon, was reported missing from her residence at Old Timers Aboriginal town camp in Alice Springs about 1.30am on Sunday after being put to bed.
A search involving about 50 police officers, members of the Northern Territory Emergency Services and a police helicopter was unable to find her on Sunday, with the search set to resume early on Monday.
Detective Acting Superintendent Michael Ordelman told reporters it was probable Sharon wandered out of her home but police were not ruling out suspicious circumstances.
Because of the amount of time Sharon had been missing, police held "mounting concerns" for her safety, he said.
The town camp was by the Todd River where it was easy for a child to become lost, Supt Ordelman said.
Police had been unable to find other members of the camp, he said.
"We're not saying that's nefarious, but as I said, we're not ruling out anything," he said.
Police have appealed to the public to contact them with any information that may lead to finding Sharon.
The NT Police Tactical Response Group was expected to travel to Alice Springs on Monday morning to assist.
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