A manhunt for recently released prisoner Jefferson Lewis has ramped up after a search party discovered a body before midday on Thursday, about 5km from where the five-year-old girl disappeared.
Police said the body was believed to be that of the girl, referred to as Kumanjayi Little Baby at her family's request, pending formal identification.
The heartbreaking find followed days of intensive land and air searches across harsh desert country surrounding Alice Springs.
"This is an incredibly distressing development," NT Police Commissioner Martin Dole told reporters.
"(Her) family has been formally notified and our thoughts are firmly with them at this devastating time.
"I want to be clear, we are not in a position to provide answers as to the cause of (her) death or how long she has been deceased."
Kumanjayi vanished after being put to bed at a residence in the Old Timers camp near Alice Springs on Saturday night.
It sparked a major search for the non-verbal girl and 47-year-old Lewis, who police suspected abducted the child just six days after being released from prison.
Her body was discovered on the fifth day of a widespread search.
Assistant Commissioner Peter Malley said forensic testing on items seized from the crime scene had strengthened their focus on Lewis.
He said a pair of child's underwear found during the investigation had been linked by forensic analysis to both Lewis and the girl.
"The focus right now is to locate Lewis – it is our sole job in this investigation right now," he said.
In a stark message to the suspect's relatives, Mr Malley urged them not to harbour or assist him.
"To the family of Jefferson Lewis: we believe he has murdered this child - do not assist him," he said.
"Get him to the police station and we'll look after him. And I'll say to Jefferson Lewis: we're coming for you."
Police previously said there were people in the community who "absolutely know" where Lewis was and urged them to contact police.
They had been adamant that Lewis was still in the Alice Springs area, warning anyone sheltering him would face charges.
Lewis was sentenced to 64 months in prison, between 2016 and 2025, for offences including aggravated assaults, breaching domestic violence orders, bail and resisting police.
Scores of police, emergency services workers, defence personnel, Aboriginal trackers and community volunteers had scoured the area with helicopters, drones, horses, dogs and all-terrain vehicles during the search for the girl.
Police said support from the Alice Springs community and from across Australia had been "overwhelming", urging locals to continue supporting one another as the investigation entered its next phase.
A post-mortem examination, expected to be conducted within days, will be crucial in determining the cause and timing of the girl's death, police said.
A coronial process and full criminal investigation are now under way.
Pathologists will look for signs of injury, trauma and any trace evidence that could further connect Jefferson to the death, with results to feed into both the homicide investigation and a future coronial inquiry.
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