Daystar University has been closed indefinitely following a two-day boycott of classes by students.
All undergraduate and diploma students were ordered to vacate the university with immediate effect.
Post-graduate programmes have, however, not been affected by the new directive.
The students were protesting deteriorating conditions at the university which they maintain the administration has refused to fix.
They specifically cited a poor state of facilities and a fee hike.
Vice Chancellor Timothy Wachira was accused of refusing to listen to the students' complaints.
The Student Government, the Daystar University Students Association (DUSA), has also been suspended with immediate effect.
General Service Unit (GSU) officers arrived at the university's Athi River campus to ensure the protests did not get out of hand.
The student union President, Aloys Otieno, claimed live bullets had been fired at them.
He took to social media to state: "Live bullets being used in Athi River!! Police have been sent to arrest me in Valley Road!"