Hundreds of pupils had stormed out of school in the middle of the night to go to the district commissioner's office to demand better conditions.
The BBC's Wanyama wa Chebusiri in Nyeri says three of those attacked are critically ill in hospital.
The victims say as they were marching a gang of local villagers attacked them, raping at least 15 girls in turn.
"Unfortunately their screams could have been confused with the excited shouts of protesters," a student on the march told Kenya's East African Standard newspaper.
Our correspondent says almost 700 Kanguburi Girls High School pupils chose to make the 10-15km walk at night to disguise their identities.
Police say they are investigating the matter, but no arrests have been made.
The school's headmistress spent much of Monday in an emergency meeting with local education authorities, our reporter says.