Jefferson Lewis, 47, was flown to Darwin for safety reasons after an angry crowd attacked him and then tried to storm an Alice Springs hospital where he was taken after his arrest on Thursday night.
One rioter has been arrested and more charges are expected, police said.
Takeaway alcohol has been banned in Alice Springs on Friday and sales will be limited on Saturday as authorities attempt to quell the unrest.
Police had called on all the resources available to contain the violence following Lewis' arrest, Northern Territory Police Commissioner Martin Dole said on Friday.
He said rioters would face the law "just as Jefferson Lewis is facing the law".
Mr Dole appealed for calm and strong leadership to ensure the behaviour was an aberration, not a pattern.
"The behaviour that we saw last night cannot be explained away, excused or accepted - there is absolutely no excuse for violence against emergency services that are just doing their job."
Lewis was arrested on Thursday night hours after the discovery of a child's body about 5km from where a girl disappeared near Alice Springs on Saturday night.
The discovery followed an intense five-day search for the missing five-year-old, now referred to as Kumanjayi Little Baby at her family's request, in line with cultural traditions.
Northern Territory Chief Minister Lia Finocchiaro backed police, saying while the community is angry and grieving, "there is never an excuse or an acceptability of violence as a response".
She says she does not want the riots to overshadow what she called an "incredible community effort", with hundreds of people walking "shoulder to shoulder" in the search for the missing girl.
Alcohol sales on Sunday will remain highly restricted and Monday and Tuesday will continue as "grog‑free" days in a bid to support the community and reduce pressure on frontline workers.
Tensions erupted after Lewis was found at a town camp at about 10.30pm on Thursday when he identified himself to people there, the commissioner said.
He was beaten by vigilantes and unconscious when police arrived to arrest him and were also attacked with about 200 people turning on emergency services.
After being taken to hospital about 400 angry people gathered and tried to get inside to "get to Jefferson Lewis".
Two police officers, two paramedics and a fire and rescue officer were injured in the disturbance.
Tear gas was deployed as projectiles were thrown at officers and police cars damaged, including one that was torched.
Lewis was flown to Darwin for his own safety as well as that of Alice Springs hospital staff, Mr Dole said.
Indigenous Australians Minister Malarndirri McCarthy called for calm among the community as a family began the cultural grieving practice of "Sorry Business" and justice took its course.
Prime Minister Anthony Albanese said the girl's death was devastating for the Alice Springs community.
"She was just at the start of life's adventure. This is the tragic outcome we were all desperately hoping against," he posted on social media.
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