The anti-graft agency is investigating 18 public universities over various offences including theft of public funds, unethical conduct and academic fraud.
Ethics and Anti-Corruption Commission (EACC) spokesperson Erick Ngumbi said that investigations are at different stages although he did not give details of the public universities on the radar of the agency.
This comes when many public universities face serious financial challenges and cumulative debts of over Sh70 billion.
However, Mr Ngumbi said that an account holding Sh74 million belonging to Jaramogi Oginga Odinga University of Science and Technology (JOOUST) has been frozen by the High Court as the EACC conducts investigations into alleged corruption at the university.
Former vice-chancellor Prof Stephen Agong is the centre of EACC's investigations, which suspect him of colluding with contractors and consultants to defraud the institution during his tenure in office.
Mr Erick Ngumbi said that investigators had retrieved vital documents after conducting a search at the three homes of the former VC in Nairobi, Kisumu and Homa Bay counties.
"Upon the expiry of Prof Agong's contract at the university, he carried away all the documents relating to various construction contracts for the university, both in soft and hard copies," said Mr Ngumbi.
The scandal which also involved a former deputy vice-chancellor and four other top officials at the institution of higher learning has since seen JOOUST account frozen by Siaya High Court after the contractor accused the varsity of failing to pay a contractor Sh179 million.
"The contractor took advantage of the situation to demand more funds while the documents recovered indicate that all their dues had been settled, despite the projects not being fully completed as per the contract," said Mr Ngumbi.
He said that the commission would go to court to seek a review of the order freezing the university accounts.
"When the contractor went to court, the university could not defend the case since the retired vice chancellor left office with all the original documents relating to the project which EACC has since retrieved,” said Mr Ngumbi.
He noted that litigations have affected the running of the university. The projects affected include a 1,000-capacity men's hostel, an ultra-modern library, a science laboratory, an administration block, a research complex and a tuition block. Procurement of security services is also involved in the myriad of malpractices being investigated by the anti-graft agency.
Mr Ngumbi spoke to the press in Ugenya Constituency, Siaya County while attending the burial service for the late Mama Joyce Oginde, mother of EACC chairperson Dr David Oginde.
EACC is also investigating an alleged loss of Sh2.2 billion at Moi University. Mr Ngumbi indicated that 59 people, including the VCProf Isaac Kosgey , have recorded statements with the commission.
"Four university council members have been summoned to record their statements on Wednesday and Thursday, this week," he said.
At the University of Nairobi, the EACC is investigating allegations that the university council irregularly created a senior position and appointed a person without the requisite academic qualifications to serve as its chief operations officer.
Mr Ngumbi said EACC has given the university 30 days to take administrative action to remedy the situation, as investigations continue.
