Jefferson Lewis, 47, has been accused of killing Kumanjayi Little Baby, the name used for the child after her death at her family's request in line with cultural tradition.
The girl went missing from a home on an Indigenous town camp near Alice Springs, sparking a massive five-day bushland search for both her and Lewis.
The 47-year-old had been out of prison for six days when she disappeared.
The five-year-old's body was found in bushland on Thursday, prompting an outpouring of grief and anger across the community.
Lewis was arrested later that day in an Alice Springs town camp after being beaten unconscious by locals.
He was taken to hospital, where tensions continued to rise as residents demanded access to him and called for immediate traditional justice.
Five emergency service personnel were injured in the resulting unrest, with police vehicles and ambulances damaged.
For his safety and that of hospital staff, Lewis was later flown to Darwin by the NT Police air wing.
He has been remanded in custody ahead of an expected appearance in Darwin Local Court on Tuesday.
Police confirmed the charges at a media conference on Sunday, describing the case as deeply distressing for the girl's family and the wider community.
NT Police Commissioner Martin Dole said detectives worked around the clock on what he described as an extensive and complex investigation.
"Our thoughts are firmly with Kumanjayi's family, loved ones and the wider community that have been deeply impacted by these events," he told reporters.
Police urged the public to respect the legal process, admitting the case had shaken the community.
"It's deeply distressing, not only for the family, but for the wider community," the commissioner said.
"This is a horrific event and a horrific set of circumstances."
Police are also investigating looting and violence that erupted after the arrest, including attacks on emergency services and extensive damage to local businesses.
Officers have released footage showing people breaking into shops and stealing stock, with the commissioner insisting the behaviour captured on video had nothing to do with grief or cultural law.
"What you will see is criminal behaviour, plain and simple," he said.
"It's abhorrent, it's disgusting and it will not be tolerated or accepted by the Northern Territory Police - and it should not be accepted by the community."
Police estimate more than $200,000 worth of goods have been stolen with the final damage bill expected to rise as structural damage is fully assessed.
Two people have handed themselves in and several others have been arrested, with more charges expected as investigators review hundreds of hours of footage.
Officers are also looking for people they believe sheltered Lewis before his arrest.
Community elders and the girl's family have called for calm and urged people to let the courts deal with both the alleged murder and the unrest.
Authorities imposed temporary takeaway alcohol restrictions in an effort to prevent further violence, and police say they will maintain a strong presence in Alice Springs and surrounding communities in coming days.
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