The head teacher of Groupe Scolairie (GS) Nsinda in Rwamagana district has been suspended following reports that 26 students were found to be pregnant, among other allegations.
Emmanuel Usabye was asked to stay away from the school last week. He is also accused of neglect of duties and financial irregularities.
The minors were either found to be pregnant or recently gave birth while at school, according to officials.
The Police are investigating the allegations.
Francois Ndayambaje, the chairperson of Parents Committee, said the suspension would pave way for investigations.
"I discovered financial irregularities and high level negligence by the head teacher. His suspension long overdue. I gave the financial irregularities report to the police," Ndayambaje said.
A teacher, who wanted to remain anonymous, said the school's top administrators were blase to goings-on in the school.
The teacher linked some of the pregnancies to one of the former school administrators, who allegedly committed suicide last year.
"Teenage pregnancy here began in 2011. No one cared and yet this school is just a stone throw away from district education offices," the teacher said.
Ndayambaje acknowledged that they had received reports of misconduct of some members of staff, but blamed parents for not being strict on their children.
"With such levels of teenage pregnancies, we are heading nowhere as a community. The administrators gave bad example to children," he said.
Theophile Cyiza, the chairperson of the Forum to Combat HIV/Aids and child pregnancy in Muhazi sector, said they blew the whistle after testing the children two months ago, adding that some students had caesarean births because they were too young for normal delivery.
The State Minister in-charge of Primary and Secondary Education, Dr Mathias Harebamungu, also acknowledged that he had received reports of child pregnancy in the school. He blamed district leaders for not acting fast to address the issue.
"It is unfortunate that local leaders took all this long to take reaction. Otherwise, we started a campaign with stakeholders to check teenage pregnancy in schools couple of years ago," Harebamungu said.
The district mayor, Nehemie Uwimana, said suspension of the head teacher would ensure activities in the school are not compromised during the investigations.
He reassured parents, who were shocked and unsettled by the news, that the priority is being given to the smooth running of the school.
Meanwhile, the Governor of the Eastern province, Odette Uwamariya, has commissioned a separate select committee to investigate the allegations.
Uwamariya said anybody implicated in the scandal would face the law.
"It is disgusting to hear what happened to the girls. I want to see to it that culprits are brought to book," she said.