An Indigenous man has died after being restrained by police in custody in Mparntwe/Alice Springs.

The man, who Guardian Australia has identified as a 24-year-old Aboriginal male from the town, died on Tuesday.

NT Police said the man had been "involved in an altercation with a security guard at the Coles supermarket" in the CBD at around 1:10 pm.

They said two officers were in the store and "restrained the adult male", but argued that a short time later, he "stopped breathing and CPR was commenced".

"St John Ambulance attended the scene, and the man was conveyed to Alice Springs Hospital where he was pronounced deceased shortly after 2:20 pm," the NT Police said.

There have been almost 600 Indigenous deaths in custody since the 1991 Royal Commission; currently, no one has been found guilty for any of them.

NT Police say a crime scene has been established, and the shopping centre is expected to remain closed.

"The incident is being investigated as a death in custody," they said.

"The NTPF Major Crime Section Detectives are travelling to Alice Springs and investigations are ongoing. Police will now investigate this matter on behalf of the coroner."

Speaking in Darwin on Tuesday afternoon, Assistant Commissioner Travis Wurst said the man was placing items in his clothing when he was confronted by security guards, the ABC reported.

Mr Wurst argued that one of the security guards was assaulted before the two police officers, who in plain clothes, "rendered assistance to the security guards".

"The male behaved rather aggressively and was placed onto the ground by those police officers; he was later identified as losing consciousness," he said.