A total of 29 initiates died during the summer initiation season, while nine traditional surgeons and nurses were arrested.
The initiates died from dehydration, sepsis and assault.
Despite the high number of deaths, the figure is still down from 2015, when 46 initiates lost their lives.
Traditional Affairs spokesman Mamnkeli Ngam said although the figure had dropped, the government and traditional leaders remained greatly concerned.
“One death is too many. The custom does not kill, but it is the ill-treatment of initiates by those who have criminal tendencies that put a dent in the ancient rite.
“Every season we work very hard, doing awareness campaigns, pumping millions of rand into this, only to be disappointed by those who do not care,” Ngam said.
The Chris Hani district, which in 2015 recorded 19 deaths, had the most this summer with 12.
The other districts’ figures were: Amathole 4,O R Tambo 4, Alfred Nzo 4, Joe Gqabi 3, Buffalo City 1 and Nelson Mandela Bay 1.
Ngam said he prayed that no more deaths would be reported as the season came to an end.
“The last batch of initiates graduated this past weekend.
“They have been reunited with their families and are preparing to go back to school and tertiary institutions as the academic year starts this week.
“But there are those few initiates still in the mountains,” he said.
While provincial initiation monitoring teams had returned home before Christmas, Ngam said traditional initiation forums continued to monitor the rite.
The province is due to hold an evaluation summit next week for traditional initiation at which stakeholders will seek solutions to the problems that emerged over the course of the season.
Ngam said awareness campaigns would continue in preparation for the winter season, starting with programmes to enforce the Customary Initiation Act, which was enacted in November.
“The act will be in full swing and we have to embark on numerous campaigns to make sure that stakeholders know their roles and responsibilities as enshrined in the act.
“The role of traditional leaders is clearly defined [and] the roles of traditional surgeons and nurses are clearly stated.
“So people will be arrested and charged for failing to [carry out] their responsibilities.
“We will go around teaching people about the new act,” Ngam said.