Universities had not remitted at least Sh7.5 billion of employees' deductions to relevant agencies by June 2017, according to an audit report by Ministry of Education.
The amount includes Sh4.5 billion of employees' pension and Sh2.6 billion of PAYE.
Sacco deductions totalling Sh481.2 million could also not be traced.
Employees of named public universities are also locked out of national health cover as Sh4.2 million deducted from their monthly pay is yet to be submitted.
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Affected universities include UON, KU, Jkuat, Tuk, Multi Media University, Egerton University, Rongo, Taita Taveta, Kaimosi Friends, Maasai Mara and Murang'a University College.
The audit report, for instance, shows that UON had not remitted Sh1.3 billion of pension funds, with JKUAT sitting on Sh1.09 billion.
Kenyatta University could not account for Sh902 million P.A.Y.E deductions followed by UON which had not submitted Sh704.5 million.
At least Sh187.9 million Sacco deductions from Egerton University and Sh178.9 million from the Technical University of Kenya are pending.
The former Kenya Polytechnic has also not remitted Sh3.2 million of employees' NHIF funds.
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