Neil Andersson and Ari Ho-Foster, of the CIET trust in Johannesburg, conducted the study in 1,200 schools across the country at the end of 2002.
The study has revealed shocking truth about endemic sexual abuse of male kids that has been suspected but until now only poorly documented.
"This study sought to document the prevalence of sexual violence among school-going males," Andersson said.
"We found a marked difference between the provinces of South Africa, with the least economically developed province, Limpopo, suffering the highest rates and the most developed area, Western Cape, the lowest," he added.
Researchers also found that there were systematic differences between rural and urban areas in frequency and type of perpetrator.
Some 28 percent of victims said a non-family member or teacher was the perpetrator.
Another 28 percent had been forced by a fellow student, while 20 percent had been abused by a teacher and 18 percent by an adult family member.
The researchers have warned that 'the likely consequence of all this for South African society is the multiplication of sexual abuse, since it is well established that people who have been sexually abused are more likely to become abusers themselves.
"One in ten schoolboys who took part in the study admitted they had forced sex on someone else," they added.
The researchers pointed out that until to 2007, forced sex with male children in South Africa did not count as rape, but as 'indecent assault', a much less serious offence.
They welcomed the change in legislation as a very necessary first step, but they said that 'this is far more than a legal issue', and suggested bringing it to the open and raising awareness among South Africans.
"Most of all, the rape of children calls for decisive investment in prevention. Reducing overall sexual violence will likely also pay dividends in reduction of HIV/AIDS," Andersson said.
The researchers also noted that, 'as it becomes more acceptable for male children to report sexual abuse, we have to expect a massive increase in workload for help services like Childline. They will need support to meet this demand'.
The study is published in BioMed Central's open access journal International Journal for Equity in Health.