Jefferson Lewis, 47, was arrested on Thursday night following the discovery of a child's body about 5km from where a five-year-old girl disappeared near Alice Springs on Saturday night.
The discovery followed five days of intense searching by police, emergency services personnel and community volunteers.
Police believe the body to be that of the missing five-year-old girl, now referred to as Kumanjayi Little Baby at her family's request, in line with cultural traditions.
Lewis was flown to Darwin on Friday morning after riots broke out in Alice Springs overnight, Northern Territory Police Commissioner Martin Dole told the ABC.
He said attacks on emergency workers outside the Alice Springs Hospital, where Lewis was taken after his arrest, were not reflective of what had been seen from the local community in the past five days.
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.
He said the community was mourning but the "violent outpouring" and the attacks on emergency workers were not acceptable.
Lewis was found at a town camp at about 10.30pm on Thursday after 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.
"They were turned on by about 200 people. They were able to get out of there and get Mr Lewis to hospital," Mr Dole said.
"Then we saw about 400 angry people gather at the Alice Springs Hospital and try and get inside and get to Jefferson Lewis."
Two police officers, two paramedics and a fire and rescue officer were injured in the disturbance.
Alice Springs was calm on Friday morning and no arrests had been made but inquiries into the riots were continuing, Mr Dole said.
"Please let the police do their job, this man is now in custody, and please do not do anything to jeopardise a future prosecution."
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.
"It must not be jeopardised by foolishness in terms of the work that has to be done by police to get this investigation done appropriately," the senator said.
Lewis is accused of abducting the girl from an Aboriginal town camp on the outskirts of Alice Springs just six days after he was released from prison.
The girl's disappearance sparked one of the NT's largest searches, with almost 200 people scouring harsh desert country for the non-verbal child and Lewis.
A pair of children's underwear found in the search has been linked by forensic analysis to both Lewis and the girl, police said.
A post-mortem examination will be crucial in determining the cause and timing of the girl's death, police said.
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.
"May Kumanjayi Little Baby live on in every heart she ever touched."
The girl's family paid tribute to her, thanking everyone who took part in the search.
"I know you are in heaven with the rest of the family," the mother said in a statement.
"Me and your brother will meet you one day. We are giving our lives to Jesus.
"It's going to be so hard to live the rest of our lives without you."
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