An Aboriginal man has died in west Melbourne's Port Philip Prison after receiving hospital treatment.

The man in his 30's died in the medical unit of the maximum-security prison on Wednesday evening, having only been transferred to St Vincent's Hospital for treatment earlier that same day.

In a statement, a Department of Justice and Community spokesperson confirmed the death.

"It is with great sorrow that Corrections Victoria acknowledges the passing of a prisoner at Port Phillip Prison," the spokesperson said.

"As with all deaths in custody, the matter has been referred to the coroner, who will formally determine the cause of death."

There is a significant overrepresentation of Aboriginal and Torres Strait Islander people in Australia's justice system.

First Nations Australians make up 30 per cent of Australia's prisoner population yet only three per cent of the Australian population, with Victoria's Indigenous inmate population tripling in the past decade.

There have been 489 recorded deaths of Indigenous people in custody since the Royal Commission into Aboriginal Deaths in Custody, which was held 31 years ago.