Sharon Granites disappeared from her home near Alice Springs early on Sunday morning, sparking a desperate search.
Police on Monday said they suspected the little girl had been abducted as they launched a manhunt for 47-year-old Jefferson Lewis.
He was staying at Sharon's Old Timers Aboriginal town camp residence and went missing at the same time of her disappearance, police said.
"We do believe Sharon has been abducted," Acting Commander Mark Grieve said in Darwin on Monday.
The little girl was last seen by her family when she was taken to bed about 11.30pm on Saturday.
She was reported missing about two hours later.
Northern Territory Senator Jacinta Nampijinpa Price backed police's calls for the outback community to come forward with any information they had to help find Sharon.
"This is every parent's worst nightmare," she posted on Facebook, saying her thoughts were with the family.
"Police have now issued an updated call for information, confirming extensive searches have been conducted but she has still not been located.
"If you know anything - no matter how small - please come forward ... let's help bring her home."
Mr Lewis was not in prison for child-related offending before being released but had a history of assault and domestic violence charges, Mr Grieve said.
"If he is involved, we certainly hope that no harm has come to Sharon," he said.
"Obviously, it's a terrible situation to have such a young child go missing.
"We want to find Sharon healthy and we want to get her back to her family."
Major crime squad detectives from Darwin have flown in to Alice Springs to investigate.
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