Romain Farina, 46, previously the head of the Mas de la Raz school in Villefontaine, in southeastern France, had been charged with various sexual offences and placed in detention in March 2015.
On Tuesday he was found dead in his cell in Corbas prison, near Lyon, on Tuesday morning after apparently having hanged himself.
According to L'Express newspaper he was being closely watched because of the risk he could commit suicide.
"You could pass every five minutes to check but there is never zero risk," said prison warden union leader Pascal Rossignol.
Farina had confessed to having tricked pupils during a workshop on experiencing new tastes when he would blindfold them and put his penis in their mouths.Video clips found at his home confirmed what had happened.
What had angered parents the most was that Farina obtained his job at the school despite a 2008 conviction for possessing child pornography.
At the time the thunderbolt rocked France and prompted the education ministry to launch an internal investigation parallel to the legal inquiry to discover how the convicted offender was hired and ended up becoming a primary headteacher who went on to rape several pupils.
Prosecutors said the school principal 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-old's complained to their parents about what they had experienced.
Justice officials say Farina 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.
In total, investigators spoke to 61 potential victims from several different schools where Farina had worked.
The school principal initially denied the alleged rapes, which are suspected to have taken place between December and March 2015 in Villefontaine.
But searches of the his home following his arrest uncovered child pornography and video clips supporting claims he blindfolded pupils and put his penis in their mouths.
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 specialized 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.
The school's supervisor, Dominique Fis, said at the time of his arrest that local officials had received no information that Farina 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 Farina had initially been hired by a school in Grenoble in September 2008, and joined Villefontaine's Mas de la Raz school in late 2014.
"He stopped working between 2008 and 2011, having taken a leave of absence after losing a child."
After Farina's arrest in March 2015,1,200 people participated in a march in Villefontaine in support of the victims.