Five boys were rescued from an illegal initiation school in Mdantsane near East London on Tuesday, the Eastern Cape health department said.
Spokesperson Sizwe Kupelo said a joint operation between the department and Eastern Cape police rescued the boys.
Police received a complaint from one of the boys' parents after the child failed to arrive for school on Tuesday.
The parent discovered her son had been circumcised at the initiation school.
The National Circumcision Act regulated the traditional custom in the Eastern Cape, Kupelo said.
Only boys 18-years-old or older may be circumcised by traditional surgeons and these surgeons had to obtain permission from the department to carry out circumcisions.
Police were searching for the traditional surgeon and accomplices who had been responsible for the illegal circumcisions and for the illegal initiation school.
During the past winter months 22 boys lost their lives as a result of botched circumcisions and a further six died after the school they were attending burnt down.
"The department of health is fully aware that it is not the custodian of the custom but our intervention is necessitated by the deaths from circumcision-related complications," he said.
The recent deaths were the reason behind the department's pro-active approach to curb the illegal occurrences.
Kupelo warned parents and the community that those who continued to disregard the law would be arrested.
Sapa