Jefferson Lewis, 47, has been charged with murder and other offences after Kumanjayi Little Baby was found dead in bushland near Alice Springs on Thursday, five days after she went missing.
Kumanjayi, the name used in line with cultural tradition after her death, Â disappeared from a home in an Indigenous town camp, sparking a massive land and air search.
Lewis was arrested later on Thursday at another Alice Springs town camp after being beaten unconscious by locals.
Police took him to Alice Springs Hospital where a large, angry crowd gathered outside demanding he face traditional justice.
Five emergency service workers were injured and police vehicles and ambulances were damaged in the rioting, while nearby businesses were looted and trashed.
Lewis was evacuated to Darwin by the NT Police air wing for his own safety and that of hospital staff.
On Sunday, he was charged with murder and other offences ahead of an expected court appearance during the week.
Police continue to investigate looting and violence that erupted following Lewis's arrest, including extensive damage to local businesses.
They have released footage of chaotic scenes as dozens looters pour into a service station and steal stock.
The station was trashed and staff cars were also damaged.
NT Police Commissioner Martin Dole insisted the behaviour had nothing to do with grief or cultural law.
A number of people have handed themselves in and more than a dozen arrests have been made over the unrest, with more charges expected as investigators review hundreds of hours of CCTV and body-worn video.
Accused looters were being charged with aggravated burglary and stealing, police said.
Officers are also searching for people they believe sheltered Lewis before his arrest.
Kumanjayi Little Baby's grandfather, senior Warlpiri Elder Robin Japanangka Granites, called for calm and asked politicians to respect the family's "sorry time", a reference to a period of cultural mourning.
He said the family was relieved a man would face court over the death of their "little queen".
"We must now let the justice system do its work," Mr Granites told the ABC.
"We do need to work together on this, on many issues facing our people and communities here in central Australia.
"But our little baby's passing must not become a politician's issue or an argument."
The girl's death has spurred calls from the federal opposition for a review of conditions within town camps and money spent on the sites, as well as for a royal commission into the abuse of Indigenous children.
But Prime Minister Anthony Albanese has doused calls for an inquiry, saying his government's $4 billion in spending on remote housing was already improving living standards.
A candle-light vigil for Kumanjayi Little Baby is due to be held on Thursday evening with participants asked to wear pink, the young girl's favourite colour.
The mood in Alice Springs was sombre but there was a determination to support one another, particularly the grieving family, mayor Asta Hill said.
"Our absolute focus right now is on a town that is in distress but also on a town that is steered toward calm and healing," she told the ABC.
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