Education Cabinet Secretary Amina Mohamed has ordered investigations into alleged misappropriation of Sh10 billion meant for staff salaries last year.
In a drastic move, Ms Mohamed set up a multi-sectoral team to audit the expenditure of the funds following lecturers' claims that up to 26 universities diverted the money into illegal expenditure.
The Sh10 billion was awarded to lecturers after two work stoppages last year that heavily threw academic programmes into disarray.
The investigations team will draw membership from the ministries of Education and National Treasury, Commission for University Education and the Kenya National Audit Office, Ms Mohamed said.
She added the team is expected to submit a report to her office within one month.
"We aren't taking anything for granted," Ms Mohamed said.
"Only after the findings are submitted to my office shall we know the veracity of the lecturers' claims and decide whether any action needs to be taken," said the CS, who was accompanied by university education Principal Secretary Prof Ntiba Micheni.
Appearing before the National Assembly's Education Committee early this month, the Universities Academic Staff Union (Uasu) officials claimed only six universities had strictly implemented the order that gave lecturers a pay increase for 2013-2017 collective bargaining agreement (CBA).
The six universities that the lecturers listed as having fully implemented the deal included Nairobi, Jomo Kenyatta University of Agriculture and Technology, Kenyatta, Maseno, Jaramogi Oginga Odinga and Pwani.
The other 25 implemented the new pay for partially before reverting to the older salaries that were outside of the CBA.
But on Thursday, Ms Mohamed appeared clearly determined to get to the root of the claims, telling the committee that was chaired by Malulu Injendi (Malava MP) she would look into the matter.
The money was released by the National Treasury in 2017 to implement the agreement.
The government released Sh4.8 billion to universities during the first supplementary budget of 2016/2017 financial year and the second instalment of Sh5.23 billion was released to universities at the beginning of current financial year.
"The ministry has since paid all salary arrears and factored the increment in the budget going forward," Ms Mohamed told the committee on Thursday.
Uasu Secretary-General Constantine Wesonga, in the petition, said the failure to complete the internal 2013-2017 CBAs and the 2017-2021 CBAs and remunerate staff in accordance with the deals is in clear breach of the terms and conditions of service for the academic staff.
Those affected were professors, associate professors, senior lecturers, lecturers, assistant lecturers, tutorial fellows and graduate assistants.
Ms Mohamed admitted that Sh4 billion for pension of university staff was yet to be paid since 2010 but promised that the government was working on the issue.
Public universities run a contributory pension scheme, to which individual lecturers pump in a portion of their monthly salary.
The individual universities contribute an equal or double share of the lecturers' salaries.
It also emerged that all the public universities have been ordered to surrender their payroll data, but only 15 complied.
Ms Mohamed also appeared to shatter the dreams of lecturers who have been pushing for mortgages.
"Whereas government policy provides for mortgages and car loans for public servants, including public universities, the existing guidelines required universities to set aside funds for the same within their available budgets," she said.
Mr Injendi and Tinderet MP Julius Melly asked the CS to bring order in the sector, saying the mess is a shame.
The CS admitted that all is not well in the sector and promised to put order saying parents and government are putting a lot of investment.
Ms Mohamed further noted postgraduate programmes had collapsed as a two-year programme was now taking several years for students to complete.
The CS also promised to address the issue of universities failure to remit statutory deductions to various agencies, warning that it is a criminal offence.
Last week, universities cited lack of money as the reason they had failed to implement pay deals.