Police have charged Jefferson Lewis with the murder and sexual assault of five-year-old Kumanjayi Little Baby.
Lewis, 47, is suspected of taking Kumanjayi Little Baby from a house at Old Timers Camp, 6km south of Alice Springs, where he was staying last week.
Police allege the 47-year-old crept into the room on Saturday where the five-year-old girl had been put to bed on a mattress, before sneaking her out via the side door sparking a massive manhunt for the pair.
Her body was found 5km south of Alice Springs on Thursday morning.
Authorities located Lewis on Thursday night with significant injuries after a group of vigilantes found him.
He was later transported to Darwin while receiving medical treatment.
NT Police Commissioner Martin Dole confirmed Lewis was formally charged with one count of murder and two counts of sexual assault on Saturday evening.
'This is a horrific event and a horrific set of circumstances and our thoughts remain strongly with the family and the community as everyone processes the impact of these horrific events,' Commissioner Dole told reporters on Sunday morning.
Police have charged Jefferson Lewis with the murder and sexual assault of five-year-old Kumanjayi Little Baby
'This has been an extensive and detailed investigation. Our detectives have been working around the clock to come up with this outcome.'
Commissioner Dole wouldn't confirm if police have identified any individuals who had assisted Lewis during his five days on the run, however said 'investigations are continuing.'
Lewis is expected to appear before Darwin Local Court this week.
It comes as five people have been arrested in relation to riotous behaviour that occurred in Alice Springs on Thursday night.
Police had to use tear gas, pepper spray and rubber bullets against the crowd which descended on Alice Springs Hospital where Lewis was receiving treatment.
NT Police said a service station and a supermarket in The Gap were subject to riotous behaviour and aggravated burglaries which caused significant damages and property loss estimated at a total of $105,000 stolen and $80,000 in damages.
'Following a review into CCTV and media outlet footage, five people aged 18, 26, 34, 46 and 49 have all been arrested and remain in custody with charges expected to follow,' NT Police said.
'Further offenders have been identified, and multiple arrests are expected to be made in coming days.'
More to come.