A high-speed chase through the Cape Flats ended in a gunfight after a car rammed pursuing traffic co.
"It is saddening to report the increased number of initiates who have lost their lives to 23," he said in a statement.
"This is despite all the efforts we have made."
Nineteen of the deceased were from the Eastern Cape, three from Mpumalanga, and one from the Western Cape.
Bapela said the 104 others were admitted for dehydration, septic circumcision, gangrene, and other related injuries.
He sent his condolences to the affected families and said government condemned illegal circumcision schools.
"The rite of passage is not a licence for abuse of the initiates but a process that is ushering these young men to adulthood and a cultural practice that needs to be respected," said Bapela.
"The ministry of co-operative governance and traditional affairs continues to call on all members of the community to report any illegal initiation schools to the police."