The estimated 33 firearms that disappeared from the from the Bellville South and Mitchells Plain police stations at the end of August will most likely end up in the hands of gangsters, Police Minister Fikile Mbalula said on Monday.
"What cannot be tolerated is violence sponsored from within the police ranks," Mbalula said in a statement.
"The people of South Africa, particularly in Cape Town, are already plagued by ugly scenes of gang violence and other serious crimes where innocent people, including children, get killed on a regular basis."
Mbalula called on investigations by the Hawks into the incidents to be completed as soon as possible.
Fifteen 9mm firearms were reported missing from the Mitchells Plain police station on August 25.
Five days later, on August 30, 18 firearms were unaccounted for in the Bellville South police station.
The Bellville South area is known as a stronghold of the Sexy Boys gang.
Guns stolen from police have been the focus of an investigation before.
Ex-police colonel Chris Prinsloo, now serving a jail sentence, previously confessed that he had sold roughly 2 000 firearms which were stolen from police stores in Gauteng. The guns were meant to be destroyed.