A provincial health department representative said "the deaths occurred over the past 12 days, with nine of them occurring over the past 24 hours," the BBC reported Friday.
In some South African communities, circumcision is seen as a rite of adult passage.
The practice, common among the Xhosa and Ndebele communities, may be reintroduced among the Zulu people if King Goodwill Zwelithini has his way because of reports that medical circumcision can reduce the chances of getting the human immunodeficiency virus, which can lead to AIDS, the BBC said.
About 60 boys from 11 initiation schools, since closed, have been rescued.
"All 60 of them have septic wounds and are dehydrated," the South African Press Association quoted Eastern Cape health representative Sizwe Kupelo as saying.
"Four of the boys even need their genitals removed completely, as it could result in death if it's not done. We are just waiting for consent from their parents to perform the procedures."
Illegal initiation schools, especially in rural areas, are set up by unregistered surgeons as a way of making money, the BBC said.
One unregistered traditional surgeon had been arrested several times for the same offense.
"He was recently given a three-year suspended sentence but he continued doing the same thing. In the past five years, close to 20 initiates died in his schools and 15 had their penises amputated," the Eastern Cape health department said.