The Department of Co-operative Governance and Traditional Affairs says some parents refuse to send their children to registered initiation schools, or get them tested before circumcision.
The department believes these factors are behind some of the deaths of young boys while they undergo the rite of passage into manhood.
The winter initiation season ended with 16 deaths across the country, with the Easten Cape recording the highest number of deaths at seven, followed by Gauteng with four, Mpumalanga with three, and the Western Cape with two.
According to the department, some deaths were as a result of dehydration, pneumonia, assaults, septicaemia and botched circumcision procedures.
Hundreds of boys were rescued from illegal schools with some suffering severe injuries from botched circumcisions. The provincial Cultural Affairs and Sport Department said the two deaths in the Western Cape occurred in Oudtshoorn on June 9, and in Hazeldene, Philippi on June 25.
Stacy McLean, spokesperson for MEC of Cultural Affairs and Sport Anroux Marais, said the family of the boy in Oudtshoorn had confirmed his death was due to tuberculosis while the initiate in Hazeldene died as a result of diabetes.