Jefferson Lewis, 47, was arrested on Thursday following the discovery of a child's body about 5km from where the girl disappeared near Alice Springs on Saturday night.
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, who had just been released from prison, was flown to Darwin on Friday morning after riots broke out in Alice Springs overnight, Northern Territory Police Commissioner Martin Dole said.
"He was conveyed by police air wing at about 3:30 this morning, and he's currently in Darwin or just landing in Darwin as we're speaking," he told the ABC.
"He's been given a fit-for-custody" after a health check, he said.
The commissioner said attacks on emergency workers on Thursday night outside the Alice Springs Hospital, where Lewis had been taken after his arrest, were "not reflective of what we have seen from the community of Alice Springs in the last five days".
Tear gas was deployed outside the hospital as projectiles were thrown at officers and police cars damaged.
Mr Cole said emergency services personnel were injured in the clashes.
Lewis was flown to Darwin for his own safety and the safety of hospital staff in Alice Springs, Mr Cole said.Â
Late on Thursday, Northern Territory Police Force said they had located and arrested Lewis at a residence in Alice Springs.
Lewis is accused of abducting the girl from a home in an Aboriginal town camp on the outskirts of Alice Springs six days after he was released from prison.
The girl's disappearance sparked one of the NT's largest investigations, with almost 200 people scouring harsh desert country for the non-verbal child and Lewis.
The child's body was found about noon on Thursday, on day five of the search.
A pair of children's underwear found earlier in the search has been linked by forensic analysis to both Lewis and the girl, police said.
Police are adamant Lewis had been helped by people in the community to evade capture.
A post-mortem examination, expected to be conducted within days, will be crucial in determining the cause and timing of the girl's death, police said.
A coronial process kicked off as the girl's family reeled from the tragedy.
Kumanjayi Little Baby's devastated family paid tribute to their beloved girl, thanking everyone who took part in the search.
"I know you are in heaven with the rest of the family," her 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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