There has been violence outside an Australian hospital where a man suspected of murdering a five-year-old girl was being treated, as police said they were "coming for" anyone who may have helped him.

Jefferson Lewis was arrested late on Thursday night local time in Alice Springs, after being seen by members of the local community and reportedly attacked.

Video shows dozens of people gathering outside the town's hospital, some throwing projectiles, with police using tear gas.

The body of the girl, who is identified only as Kumanjayi Little Baby for cultural reasons, was discovered earlier on Thursday.

She had last been seen on Saturday, when she was put to bed at an Aboriginal town camp near Alice Springs just before midnight.

Australia's national broadcaster, the ABC, reported that some in the crowd of about 400 Aboriginal people outside the hospital yelled that Lewis needed to face "payback" and accused the police of protecting him.

"Payback" is a term for traditional punishment under Aboriginal customary law in Central Australia.

Many were chanting that he should be killed for his alleged attack on Kumanjayi Little Baby, the ABC added.

Video from the scene shows crowds throwing items towards police and items being thrown. Several police vehicles appear to have been damaged.

Northern Territory Police Commissioner Martin Dole said in an update on Friday morning Lewis had been subjected to a "sustained attack" and was unconscious when police arrived and arrested him.

Dole said about 200 people turned on police and paramedics as they responded to reports Lewis was being assaulted.

Several people including members of the emergency services were injured, and at least one person had been arrested for attempting to set fire to a police vehicle with more arrests expected.

Dole said the scenes outside the hospital "cannot be explained away, excused or accepted". He earlier told ABC they were not "reflective of what we've seen from the community of Alice Springs in the last five days".

Lewis's injuries were not "significant enough to keep him in hospital" and he has been flown from Alice Springs to Darwin and taken into police custody, Dole said.

Charges are expected to be laid against Lewis in the coming days, Dole said. He also said that police were certain somebody in the community had been helping him, and warned "we're coming for you as well".

Forensic test to confirm the young girl's identity and cause of death will continue on Friday.

Kumanjayi Little Baby's grandfather called for calm on Friday.

"What has happened this week is not our way," Robin Granites, a senior Yapa (Warlpiri) elder, said in a statement. "Our children are precious, of course we are feeling angry and hurt at what has happened.

"This man has been caught, thanks to community action, and we must now let justice take its course while we take the time to mourn Kumanjayi Little Baby and support our family."

Police had been combing the nearby bush and desert for Lewis, who was released from prison six days before Kumanjayi Little Baby disappeared and vanished around the same time.

Dole said everyone involved in the search for her had been holding out hope of finding her alive.

"When we made that discover yesterday [it was] absolutely devastating for everybody involved," he said.

In a statement on Thursday, Kumanjayi Little Baby's mother, who was not named, said her daughter was loved and missed.

"It is going to be so hard to live the rest of our lives without you."

"We know you are in heaven with the rest of the family and Jesus. Me and your brother will meet you one day."

The girl's mother also thanked the dozens of people, both police and volunteers, who have spent days searching the area around Old Timers Camp - a site set aside by the government for Aboriginal people to stay in when in Alice Springs.

Using the names of deceased people, as well as broadcasting their image or voice, breaches cultural protocols around mourning in many Aboriginal and Torres Strait Islander communities and cannot be done without the permission of their families.