Two South African teachers' associations agree with the Centre of Justice and Crime Prevention (CJCP) that violence in schools is endemic.
The South African Democratic Teacher's Union (Sadtu) and the National Professional Teachers of South Africa (Naptosa) agreed that there has been substantial violence in schools.
But David Balt of Naptosa said four million was too big a number to be accurate.
"I am sure not so many pupils have been violated, though there are admittedly serious crimes in schools," he said.
The CJCP found that more than four million pupils had experienced violence in school.
It said many pupils had been bullied, raped and had their belongings stolen at schools.
The study also found that more pupils feared going to their school's toilets because they were havens for bullies.
Pupils also feared travelling to school.
The study was conducted in September 2005.
Balt said any generation of people would attest that bullying was part of growing up.
He said including such activities as "stolen belongings" was just a way of inflating figures.
"We must understand that stealing pencils is something that can happen all day but teachers are there to reinforce positive behaviour and we cannot classify that as theft," he said.
Balt admitted that violence in schools was worse than it was five years ago but said it was worse in areas that were gangster ridden and in schools that were near shebeens.
Jon Lewis of Sadtu said: "Some schools do not even have a security guard or a fence and these things are needed."
He said society in general was experiencing the worst crime ever and that was reflected at schools.