John Dunford, general secretary of the Association for School and College Leaders, said schools faced a bigger problem handling pupils on the sex offenders list than they did carrying out checks on teachers.
"Pupils are at greater risk from other pupils; there are many more pupils than teachers on the sex offenders register," he said. "It presents heads with difficult problems when it comes to sharing information with other schools and deciding how to teach youngsters, who can be sitting in the same class as their victims."
Mr Dunford said that he had encountered difficulties with pupils on the sex offenders register when he had been a head.
The TES online staffroom has been indundated with reports from teachers about sex offenders in their classes.
A secondary teacher said 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," she said "Until he carried out three sexual assaults on Year 7 girls that year."
Sexual assaults by pupils often go unreported in the press because of child protection legislation. Cases that received attention last year included that of four 14-year-old classmates arrested for raping an 11-year-old girl in Stoke Newington and a 16-year-old at Westminster City school in London jailed for raping a teacher.