Egerton University vice chancellor Prof Rose Mwonya has been suspended.
Sources at the university said she was shown the door over corruption allegations.
Prof Mwonya is accused of procurement malpractices amounting to millions of shillings, paying ghost workers, tampering with students records and irregular award of scholarships.
She is also accused of recalling the registrar academic affairs Prof Seth Owido, who had been suspended earlier this year, without consulting the university council.
Communicating the decision, acting council chairman Joshua Otieno said the VC had been given up to Monday, September 10, to vacate office to pave way for investigations.
Prof Alexander Kahi, the deputy vice chancellor academic affairs, was appointed VC in an acting capacity.
On Tuesday, Prof Kahi refused to discuss reasons for the VC's suspension but was categorical it had nothing to do with graft.
"There is nothing like corruption allegations against VC Prof Mwonya. The university does not have any money for corruption. This is not the National Youth Service," he said.