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Australian police have confirmed the discovery of a body believed to be that of a missing five-year-old Indigenous girl, sparking a manhunt for her alleged murderer.

The young girl, referred to by her family as Kumanjayi Little Baby in line with Indigenous customs, was reported missing from her remote central Australian home late on Saturday.

Authorities located the body, believed to be hers, shortly before midday on Thursday, approximately 5 kilometres (3 miles) south of the original crime scene.

Her disappearance had made national headlines, with hundreds involved in extensive land and air searches across the harsh desert terrain of the Alice Springs region.

"Our hearts are broken that the case ​of the ⁠little girl missing in Alice Springs ‌has had such a tragic ending," Prime Minister Anthony Albanese said in a statement on X.

"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."

open image in gallery Volunteers join the police and emergency services in searching the scrubland surrounding Todd River on the third day of the search for a missing five-year-old, whose family has asked her to be referred to as 'Kumanjayi Little Baby' ( AAP )

Police said the prime suspect was 47-year-old Jefferson Lewis, who had been recently released from prison and was in the area at the time of her disappearance.

"The ⁠focus right now is to locate Jefferson Lewis. It is our sole job in this investigation right now," Northern Territory Police Assistant Commissioner Peter Malley said at a news conference.

"I say to the family of Jefferson Lewis that we believe he's murdered this child. Do not assist him. Get him to the police station and we'll look after him."

"And I say to Jefferson Lewis, we're coming for you."

Malley said ‌police had seized items from the crime scene, including a pair of ​child's underwear. Forensic testing of the underwear detected DNA profiles belonging ‌to Kumanjayi Little Baby and Lewis.

open image in gallery Kumanjayi Little Baby ( Northern Territory Police )

After the body was found police released a statement from Kumanjayi Little Baby’s mother:

“To Kumanjayi Little Baby,

Me and Ramsiah miss and love you.

I know you are in heaven with the rest of the family with Jesus and the Father, Son and Holy Spirit.

Me and your brother will meet you one day.

We are giving our lives to Jesus.

It is 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.

Love from Mum and Ramsiah.”

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.