The person was an inmate at Loddon Prison near Castlemaine when they died on Sunday, authorities confirmed. Further information about the death has not been released.
"As with all deaths in custody, the matter has been referred to the coroner, who will formally determine the cause of death," a Department of Justice and Community Safety spokeswoman said.
AAP has confirmed the prisoner was Aboriginal.
Premier Daniel Andrews said he was aware of the prisoner's death.
"The death of any person in custody is of great concern to all of us," he told reporters on Tuesday.
The prisoner is the second Indigenous person to die in custody in Victoria since a 32-year-old Aboriginal man died at Port Phillip Prison in the state's west last month.
Corrections Victoria announced the 32-year-old's death on August 12.
"We recognise that all deaths in custody have impacts on family members, friends, victims and the broader Aboriginal community, and we're working to ensure they are provided with the support they need," the agency said at the time.
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