"An unknown man entered [the school] during the night and shot and killed a 22-year-old circumcision traditional surgeon," Lieutenant Colonel Mzukisi Fatyela said on Tuesday.
He said a 21-year-old man, who was also responsible for the initiates, was wounded.
"The motive is unclear," Fatyela said.
No arrests have been made and police were investigating the murder and attempted murder.
The surgeon's death came a few weeks after the spotlight fell on traditional circumcision since the death of 27 boys at initiation schools in Mpumalanga.
President Jacob Zuma in May expressed outrage at the news.
"The whole country is outraged at this massive and unnecessary loss of young life at the hands of those who are supposed to nurture and protect them," Zuma said in a statement at the time. "It cannot be acceptable that every time young men reach this crucial time in their development, their lives are culled in the most painful of ways, in the care of circumcision schools."
An effective intervention strategy cannot be put into place unless government has an indication of the state of play in each province where initiation is practiced. The practice is most prevalent in the Eastern Cape, Limpopo and Mpumalanga.
When the Mail & Guardian canvassed government officials for information on the numbers of deaths and mutilations caused by botched circumcisions each year, reporters were sent from pillar to post in search of statistics.
Eastern Cape statistics
Of the three provinces in which initiation is most commonly practiced, the M&G was only able to get statistics from one, the Eastern Cape.
In that province, the death toll for the five years from 2008 to 2012 was 323. During that time, a further 126 boys suffered genital amputations.
Sizwe Kupelo, a spokesperson for the Eastern Cape health department, said that keeping these statistics was possible because the department works together with Eastern Cape House of Traditional leaders, local government and various community structures.
The Limpopo and Mpumalanga health departments could not provide numbers and referred further questions to traditional leaders and the department of traditional affairs.
The Eastern Cape has a head start on other provinces – in 2001 it became the first province to introduce legislation regulating traditional circumcision in an attempt to curb deaths and genital mutilation taking place in the bush.
In contrast, Mpumalanga has yet to finalise its initiation Bill.
Initiation ceremonies are common in South Africa, where youths partake in various activities as a rite of passage into adulthood, usually over the course of three weeks.
About 30 000 youths signed up for initiation this year.
In addition to being circumcised, the boys and young men are put through a series of survival tests which sometimes includes exposure to South Africa's winter with very little clothing.Their faces are painted with red clay and they are given herbal concoctions to drink.
Former president Nelson Mandela described the experience in his autobiography as "a kind of spiritual preparation for the trials of manhood". – Additional reporting by Sapa