The man suspected of abducting and killing five-year-old Kumanjayi Little Baby has been flown from Alice Springs to Darwin over safety concerns.

Martin Dole confirmed Jefferson Lewis, the 47-year-old man accused of killing Kumanjayi Little Baby, was flown out early this morning. 

'Safety concerns for the hospital and medical staff, safety concerns for the police and lastly safety concerns for Mr Lewis himself.

'Our police swear an oath to serve and protect, we don't get to choose who we protect, so the safety of Mr Lewis was important as well.'

Kumanjayi Little Baby was taken from a house at Old Timers Camp, 6km south of Alice Springs, where Lewis was staying five days ago, and authorities had been searching for him since.

A local has revealed to Daily Mail how a group of vigilantes beat Lewis after spotting him lying low at Charles Creek Camp, located near the centre of town.

'A group of young boys saw him walking down the street and they noticed him as the man on the news,' the local said.

'They ran up to him and started beating him viciously. He was trying to get under a shipping container; he might have been sleeping there or just trying to get away from the mob.

'He has been beaten badly and is in a bad way. But this won't be enough, people want tribal punishment and want to keep going.'

Police intervened and arrested Lewis before rushing him to Alice Springs Hospital, where he arrived before 10pm local time. More than 100 people then gathered outside the hospital, throwing rocks at the windows as the furious crowd screamed for Lewis to be brought outside. 

They only dispersed when police deployed tear gas, but dozens remained on the street behind the hospital, with one woman claiming some attendees had 'smashed a cop car up' in retaliation. Others were seen throwing projectiles at officers.

The arrest came just hours after police discovered Kumanjayi Little Baby's remains and confirmed Lewis's 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 the young girl was allegedly abducted at Old Timers Camp on Anzac Day.