"It's a difficult issue for headteachers to deal with, particularly if the sex offender and the victim are in the same school or in the same class," Mr Dunford told EducationGuardian.co.uk."They clearly have a responsibility to help young sex offenders to develop as normal members of society. But equally they have a responsibility to other pupils to ensure their safety - particularly that of victims, so they don't have to come face to face [with their abuser]."
Mr Dunford said his comments followed conversations with many headteachers who had had dealt with young sex offenders.
The Department for Education and Skills said it had no figures on the number of children listed on the register, but a spokesman said: "Any form of abuse or violence by pupils will not be tolerated, and we fully back schools in permanently excluding and prosecuting those who use abuse or violence against anyone in a school - pupils or staff."
Yesterday the education secretary, Ruth Kelly, admitted that 56 sex offenders had been cleared to work in schools by Labour ministers or government officials since 1997. The Times Educational Supplement reported today that its online forums had been inundated with reports from teachers about sex offenders in their classrooms.
One secondary school teacher wrote that one of her pupils was placed on the register aged nine after raping his cousin. "As he had been sexually abused himself and exposed to pornography at a very young age, it was possible to feel some pity for him - until he carried out three sexual assaults on Year 7 girls that year," she wrote.
Parents have also expressed their concerns on the EducationGuardian.co.uk talkboards.
One parent said her 13-year-old daughter had been sexually harassed and assaulted by boys in her class.
"This is bullying with a potential that frightens the hell out of me," she wrote.
Last year, a group of 14-year-old boys were arrested for raping an 11-year-old at their north London school and a 16-year-old pupil was jailed for life for raping a teacher.