The headteacher has confessed to having tricked blindfolded pupils into oral sex during a workshop on experiencing new tastes.
The confession followed earlier revelations the suspect obtained his job working with young children despite a 2008 conviction for possessing child pornography.
That thunderbolt prompted France's education ministry to launch an internal investigation parallel to the legal inquiry to discover how the convicted offender was hired, and determine if any other victims were abused.
On Tuesday the Minister was expected to announce the formal dismissal of the headteacher after several other accusations of child rape were made against the man.
Prosecutors said the school principal, an unidentified 45-year-old father, had forced at least two pupils to perform oral sex acts on him during the workshop. The activity involved children wearing blindfolds and describing items they were given to taste.
Authorities were alerted after two six-year-olds complained to their parents about what they had experienced.
Justice officials say the suspect tricked at least two pupils into oral sex behind a screen at a far end of the classroom.
Under French law, the assaults are qualified as rape.
Nine complaints by nine different pupils the suspect had been teaching have been filed with police thus far, said prosecutor Matthieu Bourrette.
The school principal initially denied the alleged rapes, which are suspected to have taken place between December and March in the town of Villefontaine, near the city of Lyon in southeastern France.
But searches of the his home following his arrest Monday uncovered child pornography.
It also emerged that in 2008 he was convicted for possessing similar material, sentenced to a six-month suspended jail term and ordered to receive specialised treatment.
However, he was not banned from working with children — a fact that may have made it difficult for education authorities to find out about his past before hiring him.
'State of shock'
The school's supervisor, Dominique Fis, said local officials had received no information that the suspect was listed in France's national database of child sex offenders.
"There was nothing in his file concerning that conviction, and we only learned about it yesterday," Fis said.
Fis noted that while several employees in her administration have access to the sex offender database, consultation of the listing is only automatic "for entry level hires and interns."
"After that there is no systematic procedure," she said.
Fis said the suspect had initially been hired by a school in Grenoble in September 2008, and joined Villefontaine's Mas de la Ras school in late 2014.
"He stopped working between 2008 and 2011, having taken a leave of absence after losing a child."
The school has put a psychological support cell into place to help pupils, parents and teachers through the traumatic period.
"We've met with parents, who are in a state of shock — as is the entire teaching staff," Fis said.
Earlier Tuesday, French Education Minister Najat Vallaud-Belkacem said an administrative inquiry had been launched into how a convicted sex offender could have got a teaching job.
"We have learned about these extremely grave, indeed abominable acts," she said, promising "disciplinary panels will determine punishment" if error or negligence is discovered in the suspect being able to obtain his post.