The girl, now referred to by her family as Kumanjayi Little Baby in line with Indigenous customs, was reported missing from her home on the outskirts of Alice Springs late on Saturday.
Her body was found on Thursday by one of hundreds of people searching harsh desert terrain around the town, a popular tourist destination in Australia’s Northern Territory.
Jefferson Lewis, a 47-year-old man who police allege killed the girl, was taken into police custody on Thursday night after being found by locals and badly beaten, Northern Territory Police Commissioner Martin Dole said in an interview with public broadcaster ABC on Friday.
A crowd of around 400 people later gathered outside Alice Springs Hospital where Lewis was being treated, attempting to force their way inside, Dole said.
Local media reported police fired tear gas to disperse protesters, who threw projectiles and lit fires, including setting two police cars alight.
“The violent outpouring that we saw last night, the attacks on police and emergency services personnel, not only is not acceptable, but it’s not reflective of what we’ve seen for the last five days,” Dole said, referring to the close cooperation between locals and police during the search.
Two police officers and two medical workers were injured, he added.
Lewis was moved to the territory capital Darwin in the early hours of Friday morning for his own safety, Dole said. He is likely to be charged in the coming days.
Australia has struggled for decades to reconcile with its Indigenous population, who have inhabited the land for some 50,000 years but were marginalised by British colonial rulers.
Indigenous Australians make up around 3.8% of Australia’s population of about 27 million, but track near the bottom in almost every economic and social indicator and have disproportionately high rates of suicide and incarceration.
Thousands including the victim and her family live in communities known as camps on the outskirts of Alice Springs, where housing and services are often inadequate.
The town has occasionally ordered curfews and alcohol bans to quell unrest among Indigenous communities.