Police staff performed CPR until the ambulance arrived.
The paramedics continued to try to resuscitate him for more than 30 minutes before he was pronounced dead.
Acting Central District Commander Inspector Chris de Wattignar said it was a very sad time for all involved.
"We extend our deepest sympathies to the family. Police staff make every effort to ensure the safety of those in police custody."
A post mortem would be conducted to determine the cause of death, he said.
An investigation and policy and procedures review was underway, the incident had been referred to the IPCA and Worksafe had been notified.
Support was being offered to the man's family and the police staff involved in the incident.
The matter had been referred to the Coroner.
