Northern Territory Police have arrested Jefferson Lewis, the man investigators believe abducted and killed five-year-old Sharon Granites.

NT Police on Thursday evening confirmed the arrest of Lewis, who has spent the last five days on the run after the little girl was abducted near Alice Springs.

A vigilante group tracked down and beat Lewis, who was hiding at Charles Creek Camp.

Lewis was rushed to Alice Springs Hospital under police guard, arriving before 10pm ACST.

More than 100 people gathered outside the hospital and threw rocks at its windows. 

The news comes just hours after officers discovered the little girl's remains and confirmed Lewis' DNA was found on her clothing.

The shattering discovery was made on day five of one of the Northern Territory's biggest searches, located just 5km from where she was allegedly abducted at Old Timers town camp on Anzac Day. 

Police earlier issued a chilling warning to Lewis as they ramped up their manhunt, saying: 'We're coming for you.'

While on the run, Lewis did not have a vehicle, a phone or even a bank card, rendering modern-day investigation techniques used by police effectively useless. 

Assistant Commissioner Malley earlier on Thursday warned Lewis' relatives against helping him.

'To the family of Jefferson Lewis: we believe he has murdered this child - do not assist him,' he said.

'Get him to the police station and we'll look after him. And I'll say to Jefferson Lewis: we're coming for you.'

Mary Lewis, who is understood to be Lewis's aunt, said she hadn't seen her nephew since he was last in jail. 

'I'm sad. We are grieving. I don't know what has happened,' she told Daily Mail on Thursday.

Police previously said there were people in the community who 'absolutely knew' where Lewis was.

They warned that anyone sheltering him would face charges.

Lewis was sentenced to 64 months in prison, between 2016 and 2025, for offences including aggravated assaults, breaching domestic violence orders, bail and resisting police.

It's understood Lewis was staying at a home within Old Timers and was known to the victim's family.

Her devastated family paid tribute to their beloved girl after her body was found in bushland. They asked she be referred to as Kumanjayi Little Baby.

Kumanjayi is a substitute name used by Warlpiri people for a deceased person, avoiding the taboo of speaking their name after death. 

'I know you are in heaven with the rest of the family,' her mother, Jacinta White, 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.

'Ramsiah wants to tell you that when he sees you in heaven, he is going to give you the biggest hug ever.'

Prime Minister Anthony Albanese followed with a tribute to Kumanjayi Little Baby who was 'just at the start of life's adventure'.

'This is the tragic outcome we were all desperately hoping against,' Albanese wrote in a statement.

'No words can measure up to the immensity of the grief her family is going through. In their time of terrible loss, all Australians hold them in our hearts.

'This is devastating for the whole Alice Springs community, which came together to find her. We wish them strength, and also to the police in their difficult work as they pursue answers and, ultimately, justice.

'May Kumanjayi Little Baby live on in every heart she ever touched.'

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