Victorian authorities confirmed that the man died Sunday at the Ravenhall Correctional Centre.
Corrections Victoria said they are working closely with the Aboriginal Justice Caucus and the First Peoples' Assembly of Victoria.
In a statement, the department said the man's next of kin, as well as relevant Indigenous groups, had been told of his death.
"The family of the man were notified with our condolences, and a Smoking Ceremony is being arranged," the statement read.
His death will be investigated by the Victorian coroner.
The department acknowledged the death in custody would affect the broader Indigenous community, as well as the man's loved ones.
"We recognise that all deaths in custody have impacts on family members, friends, corrections staff and the Aboriginal community, and we’re working to ensure they are provided with the support they need."
It comes after a horror week, with a woman aged in her 50s found dead in her cell, and a 35-year-old man's death at Long Bay Hospital, involving multiple medical issues.
To the concern of many in the community, the deaths were not publicly announced by the New South Wales government - with the deaths only revealed after questioning in budget estimates.
On Wednesday, advocacy groups and Labor's spokesperson for Indigenous Australians, raised their concerns over the two deaths failing to be publicly reported, citing a lack of accountability and transparency.
Humans Rights advocacy group Amnesty International's Nolan Hunter condemned the deaths of the man and women.
Wiradjuri woman and shadow minister for Indigenous affairs Linda Burney said all states and territories should be required to publicly report deaths in custody to ensure accountability and transparency.
"There should be full transparency about deaths in custody, the idea that this was hidden or covered up, because they didn't want to cause distress or trouble in the community is not acceptable," she told NITV News on Tuesday.
There have been almost 500 Indigenous deaths in custody since 1991, when the Royal Commission into the epidemic tabled its final report.
