The 24-year-old was forced to the floor by two plain-clothes officers following an alleged shoplifting incident and assault on a security guard in Alice Springs.
The two Northern Territory officers were in the Coles supermarket about 1.10pm on Tuesday when they were alerted to a confrontation between the man and security guards in the confectionary section.
Assistant Commissioner Travis Wurst told reporters on Wednesday the man was "taken to the ground" where he remained for a number of minutes before general duties officers arrived and handcuffed him.
At that time it was determined he had lost consciousness so the handcuffs were removed and first aid, including CPR, was immediately administered.
The man, understood to be disabled, under a guardianship order and on an NDIS plan, was taken to Alice Springs Hospital where he was pronounced dead about 2.20pm.
Mr Wurst said an autopsy had been completed but the cause of death was still undetermined and a report would be prepared for the coroner.
"The police will continue to investigate this matter with an objective lens," he said.
In a statement on Wednesday evening NT Chief Minister Lia Finocchiaro said the incident was subject to formal investigation.
"My thoughts are with the family of the man who passed away," she said.
A woman who witnessed the incident but asked not to be named told the NT News: "There was an Aboriginal man on the floor and a police officer had his knee behind his head".
The man's friends were calling out "this fella has a disability, he's disabled, just be a bit more careful", she said.
"And then all of a sudden he started fitting on the ground, like he was having a seizure."
Another witness, who also asked not to be named, told the ABC they saw "a big white man" grabbing an Aboriginal man in a hold.
"It looked pretty violent and then they slammed him to the ground."
A senior relative of the man said in a statement his Warlpiri people were devastated by the death and angry that another young man had "lost his life at the hands of the police".
"What are the police doing using such force on a vulnerable young man in a supermarket? Did they even try to de-escalate?
"Why was he there alone, where were the carers who were supposed to be responsible for him?"
Outspoken senator Lidia Thorpe said it was yet another case of "brutal force" used against Indigenous people.
"He was hungry and he needed care. Instead, he was met with brutal force," she said in a statement.
"This is not an isolated tragedy - it's part of a brutal pattern where our people die at the hands of police and in prisons. We won't stop speaking out until it ends."
Amnesty International Australia called for an investigation to be conducted independently from NT Police to "ensure impartiality and to maintain public confidence in the process".
"The death of yet another young Aboriginal person in police custody is unacceptable and demands immediate action," a spokesperson for the organisation said.
The First Peoples Disability Network said the death highlighted "the increasing criminalisation of disability" and exposed failings with the guardianship system and the NDIS.
Mr Wurst confirmed the man was originally from the outback town of Yuendumu and a police cultural team was working to "understand the community sentiment" and provide information to the family.
The NT coroner is due in Yuendumu on June 10 to deliver her findings into the death of 19-year-old Kumanjayi Walker, fatally shot by then NT police officer Zachary Rolfe in 2019 during a bungled arrest.
Mr Rolfe was found not guilty on all charges over the death in 2022.
Since the 1991 Royal Commission into Aboriginal Deaths in Custody, records show 593 Indigenous people have died in custody.
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