Universities Academic Staff Union (Uasu) has threatened to oppose any attempts to renew Prof Rose Awuor Mwonya's contract as Egerton University Vice-Chancellor.
Prof Mwonya, who retired in June after attaining 70 years, is still in the office because her five-year contract ends in January 2021.
The union said the delay in appointing a vice-chancellor to succeed Prof Mwonya may create room for financial misappropriation at the institution.
The Njoro-based campus has been on the Directorate of Criminal Investigations' (DCI) radar over alleged loss of public funds.
DCI boss George Kinoti wrote to the VC on September 10, 2020, saying it is investigating the theft of public funds concerning remittances of withheld tax to Kenya Revenue Authority.
As of June 30, 2019, Egerton had accumulated Sh1.6 billion in outstanding statutory deductions.
In March, an audit report by Ms Theodora Gichana, the Inspector-General (Corporations), addressed to Education Cabinet Secretary George Magoha, exposed a deep financial crisis at the institution.
However, Prof Mwonya has dismissed the report and denied claims of corruption. "I'm reading succession politics in all the allegations levelled against me."
She also accused Uasu and some Egerton University council members of fighting her. The university has remained without a council since March and this has delayed the appointment of a new VC.
Sources from the university say Prof Mwonya's tenure,which ends in January 2021, has stirred a succession battle that has spilt over to the senate.
Subsequently, Uasu has joined the leadership row that has rocked the country's premier agricultural institution. The union wants Education Cabinet Secretary Magoha to fast-track the appointment of the new VC and members of the council to end the row.
Led by national chairperson Muga K'Olale and Secretary-General Constantine Wasonga, the Uasu national officials said there is a huge leadership vacuum in the university that needs to be fixed urgently to save the institution from slipping into a major financial crisis.
Already the debt-ridden university has slashed academic staff and non-academic staff salaries by 40 per cent to stay afloat.
However, Uasu has vowed to institute contempt-of-court proceedings against the VC for failing to obey the Employment and Labour Relations orders to prepare a new proposal on payment of 100 per cent academic staff salaries and arrears.
Uasu now wants the university management to pay its members 100 per cent salary and accrued arrears within seven days, failing which the union will issue a strike notice.
"The unfolding events at Egerton University need to be fixed and that is why we are calling on Education CS George Magoha to start the process of appointing a new VC by advertising the vacant position," said Dr Wasonga.
Dr Wasonga and Dr K'Olale spoke at the Njoro-based campus on Wednesday after attending a special general meeting convened by the Uasu Egerton chapter.
The union officials also want the Education CS to implement the audit report which calls for disciplinary action against those involved in fraud at the institution.