The Egerton University Council has suspended Vice Chancellor Rose Mwonya on allegations of financial impropriety.
Prof Mwonya was asked to stay away for 90 days pending investigations over the alleged gross misconduct.
Prof Alexander Kahi, the Deputy Vice-Chancellor Academic Affairs, has been appointed as acting VC.
He admitted receiving the appointment letter from the council to act as the VC until the matter is resolved.
The allegations which led to the VC's suspension are not limited to procurement malpractices and mismanagement related issues.
Prof Mwonya, the first-ever female Vice-Chancellor of Egerton University, took over from Prof James Tuitoek in 2015 to become the fifth VC of the institution.
Reliable sources said that the council will also investigate how some ineligible students were admitted to government-sponsored degree programmes.
The don will also be investigated on how she recalled one of the senior officials who had been suspended by the council over the admissions.
Mwonya is accused of authorising construction of a Sh70 million gate at the Njoro campus and allocating Sh180 million on the institution’s Ngongongeri farm.
The council's concern was that these projects were executed yet the varsity has cash flow challenges amid low student enrollment.
Data from the Kenya National Bureau of Statistics (KNBS) shows Egerton University enrollment declined to 11,593 last year from 13,928 in 2015.