Jefferson Lewis, 47, has been charged with murder and other offences after the body of Kumanjayi Little Baby was found in bushland near the outback town on Thursday, five days after she went missing.
Kumanjayi - the name used for the child after she died in line with cultural tradition - disappeared from a home on an Indigenous town camp near Alice Springs, sparking a massive land and air search.
Her body was found in scrub outside the town after days of searching, prompting an outpouring of grief, anger and fear in the tight-knit central Australian community.
Lewis was arrested later on Thursday at another Alice Springs town camp after being beaten unconscious by locals.
He was taken to Alice Springs Hospital under guard as tensions continued to rise, with residents calling for immediate traditional justice.
Five emergency service workers were injured and police vehicles and ambulances were damaged in the chaos.
Lewis was evacuated to Darwin on the NT Police air wing before being remanded in custody ahead of an expected appearance in Darwin Local Court on Tuesday.
Police confirmed the murder charge 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 had worked around the clock on what he called 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.
"It's deeply distressing, not only for the family, but for the wider community. This is a horrific event and a horrific set of circumstances."
NT Chief Minister Lia Finocchiaro visited the girl's mother in Alice Springs as the family began sorry business, the term used for cultural mourning.
"Right now, our focus is on a family, a town and a territory grieving - the politics can wait," a spokeswoman for Ms Finocchiaro told AAP.
The death has spurred calls for a review of conditions within town camps and money spent on the sites, including from NT Liberal senator Jacinta Nampijinpa Price.
Federal Nationals leader Matt Canavan also used the tragedy to renew calls for a royal commission into the abuse of Indigenous children and a broader inquiry into how public funds were spent in the area of First Nations affairs.
"Since the defeat of the voice (referendum), the government has effectively run scared from Indigenous policy," Senator Canavan told ABC's Insiders program on Sunday.
"You've got to get your hands dirty, get out into communities and take practical action to help people's lives, not just throw money at it."
But Prime Minister Anthony Albanese doused calls for an inquiry, saying his government's $4 billion in spending on remote housing was already improving living standards.
Police continue to investigate widespread looting and violence that erupted following Lewis's arrest, including attacks on emergency services and extensive damage to local businesses.
Officers have released footage showing people breaking into shops and stealing stock as Mr Dole insisted the behaviour had nothing to do with grief or cultural law.
"What you will see is criminal behaviour, plain and simple," he said.
Two people have handed themselves in and several others have been arrested over the unrest, with more charges expected as investigators review hundreds of hours of CCTV and body-worn video.
Officers are also searching for people they believe sheltered Lewis before his arrest as they piece together his movements during the days-long search.
Community elders and the girl's family have called for calm, urging residents to let the courts deal with both the alleged murder and the violence that followed.
13YARN 13 92 76
Lifeline 13 11 14
16°C