Police are investigating allegations by two seven-year-old girls that they were indecently assaulted by a teenager on work experience during a lesson at their primary school.
The allegations came as the Government published a Bill which will make it harder for adults who are convicted sex offenders to work in schools - but does nothing to protect pupils from other young people.
The girls attend a primary school in Wakefield which cannot be identified for legal reasons.
They separately reported to their parents on December 12 that they had been touched inappropriately during a lesson by the 15-year-old boy.
One girl said she had cried out but a supply teacher told her to be quiet and carried on reading a story to the class.
West Yorkshire police confirmed that they were investigating the incident and had interviewed the teenager. Their findings have been passed to the Crown Prosecution Service, though the boy had not been charged as The TES went to press.
The parents of one of the girls have written to Ruth Kelly, the Education Secretary, and to Elaine McHale, director of children's services at Wakefield, calling for the headteacher to be suspended pending an investigation by the council.
Both families say their daughters have behaved differently since the incident and fear it may have caused long-term psychological damage.
The father of one girl said: "She was very upset and disturbed by what happened, which is why she told her mother about it.
"At the very least a risk assessment should have been carried out to decide whether the work experience placement was suitable and what kind of supervision was required. But that didn't happen."
The parent said he was appalled at the incident his daughter had described to him, adding that the teenager should never have been placed in such a situation.
"The school system has let him down too," he said.
The primary school said it was unable to comment on the incident because of the police investigation.
Ms McHale said: "We have followed procedures set down by the local authority and are working closely with the police in this matter."
The Education Secretary was at the centre of a row in January after it emerged that 88 sex offenders had escaped supposedly automatic bans from working in schools since 1997.
The Government published a Bill entitled Safeguarding Vulnerable Groups this week which will create a new central vetting system for adults.
Schools will be able to make online up-to-the minute checks on job applicants. They will also face fines of up to pound;5,000 if they employ someone who has not been properly checked.
Several teachers have contacted The TES to say they are more concerned about sexual assaults on children by other pupils, as there are fewer safeguards to prevent them and it is harder to know if students have convictions for sex offences.
Criminal Record Bureau checks are not required on secondary pupils doing work experience in primary schools. However, there is no suggestion that the teenager accused of the Wakefield assaults had any previous convictions.
The Department for Education and Skills said: "Any form of abuse or violence in schools will not be tolerated and it is important that children are protected."