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.

More to come.

Police have charged Jefferson Lewis with the murder and sexual assault of five-year-old Kumanjayi Little Baby