Students of Moi Girls' School in Nairobi reported to school on Sunday after being closed for a week.
This after a student was reportedly raped at the institution's dormitory.
A section of parents has threatened not to take their children back without a report on what happened.
They have accused the school's management of covering up the matter.
"It is unfair that parents and stakeholders get reports from the media. If you try to inquire your child gets victimized. We are yet to come to terms with the fire incident. The rape allegations will be swept under the carpet," one said.
CS Amina on Thursday appointed a nine-member interim board to oversee the management of the school on the day Jael Mureithi opted to resign.
Deputy Principal Florence Omusula is serving in an acting capacity.