Dr Mukhwaya told Vice Chancellor Rose Mwonya not to hide under the Covid-19 pandemic to send workers home.
He said the situation at the university is the crystallisation and an aggregate of years of poor management.
A report by the university proposed the retrenchment of the staff in bid to reduce the payroll cost.
The decision to retrench the staff has also been approved by the university council.
The Kenya Universities Staff Union (Kusu) has asked Egerton University to stop plans to fire 400 employees.
The union has also called for the suspension of all top university managers and council members pending investigations into financial misappropriation at the institution.
