Violence broke out in a remote town in northern Australia after police arrested the person suspected of murdering a five-year-old Indigenous girl.

Jefferson Lewis, 47, was arrested late on Thursday night local time in Alice Springs.

The young girl, referred to by her family as Kumanjayi Little Baby in line with Indigenous customs, was reported missing from her central Australian home late on Saturday.

Authorities located the body, believed to be hers, shortly before midday on Thursday, about 5km south of the original crime scene.

Local reports said a crowd attacked Mr Lewis when he appeared in a local community and beat him unconscious before police intervened.

Police said they had long suspected that Lewis received assistance from people in the community before he appeared at a town camp.

“For him to be able to appear in Alice Springs last night just confirms to us that he was getting support from somebody,” police commissioner Martin Dole said.

“My message to those people is, look out because we’re coming for you as well.”

When officers took him to a local hospital, hundreds of “angry” residents gathered, shouting for him to be killed and demanding “payback”, according to the ABC.

The situation escalated into rioting as people threw rocks and bottles, set vehicles on fire, and damaged property. Police responded with rubber bullets and tear gas to control the crowd.

Several officers were injured in the violence.

The unrest continued into the next day, leaving streets littered with debris and signs of looting nearby. Authorities later transferred Mr Lewis to Darwin for his safety and to prevent further violence.

“As a result of presenting himself, members of that town camp decided to inflict vigilante justice upon Jefferson, and we received numerous phone calls saying he was in the process of being assaulted,” Mr Dole said on Friday.

The violence followed days of search for the girl, who had gone missing from a remote Aboriginal town camp near Alice Springs.

Hours after the girl’s death was confirmed, Mr Lewis was reportedly seen wandering near the Charles Creek town camp in central Alice Springs.

“Members of that town camp decided to inflict vigilante justice upon Jefferson and we received numerous phone calls saying he was in the process of being assaulted,” Mr Dole said.

“Our police officers were attacked at that time, as were the St John Ambulance crew that attended to assist. They were turned on by about 200 people, but they were able to get out of there and get Mr Lewis to hospital.”

Videos from outside the Alice Springs Hospital showed protesters demanding “payback”, meaning a form of traditional punishment under Aboriginal law in Central Australia.

Reports said anger within the community remained high. “The feeling is that the police are protecting this guy. They are shooting us with rubber bullets,” Harley Myers, an Arrernte man from Alice Springs, said.

“It’s like the system is not sticking up for us and letting us get our own traditional payback.”

“We’re united because it hurts all of us,” he added, “because she was only five years old and it could happen to any of our kids. I don’t want that to happen to any of our kids at all.”

Indigenous leaders, however, urged calm. “Bringing the word ‘payback’ into this scenario just fuels violence,” Michael Liddle, an Alyawarre man and Alice Springs local, told the BBC.

“There’s a system set up here, where there is a person in custody, and the Western rules will deal with that person.”

The girl’s grandfather also called for calm on Friday. “What has happened this week is not our way,” Robin Granites, a senior Yapa 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.”

On Thursday, the girl’s mother, who was not named, said: “It is going to be so hard to live the rest of our lives without you. Me and your brother will meet you one day.”

Mr Dole said charges against Mr Lewis were likely to be filed in the coming days.