At the same time, the government has admitted it cannot provide 80 per cent funding for every university student.
Machogu asked the universities to mobilise funds through other means.
He was addressing education stakeholders at the conference at the Prideinn Flaming Beach Resort in Mombasa county.
The CS said universities are facing serious financial challenges that require innovative ways to sustain operations.
"As I speak now, public universities are indebted to the tune of Sh56 billion in staff pensions and statutory deductions such as PAYE and NHIF.
"Many of the universities face challenges in paying staff salaries and their suppliers. The debts continue to pile by the day. This sorry state of affairs is a threat to the universities' ability to perform their primary mandate of teaching and research," Machogu said.
Present were the PS for Higher Education and Research Dr Beatrice Inyangala, Basic Education PS Dr Belio Kipsang, Chairman of the Universities Fund Board Prof Karuti Kanyinga and university heads.
Dr Inyangala said education is a constitutional right for all citizens and that is why her department is focused on transforming the sector to increase access to quality and relevant education.
Machogu said due to the sorry state of affairs, the Kenya Kwanza administration is in the process of undertaking comprehensive reforms in the education sector, including in the higher education sub-sector, through the Presidential Working Party on Education Reform.
The CS said since 2017, the number of students qualifying for university has been growing with the matching need for increased government funding.
He noted that 173,345 students who attained C+ and above last year would increase the number of university students funded by the government to 599,349 students if all of them are sponsored by the State.
Machogu said in this financial year, the funding requirement for public universities is about Sh71 billion against an approved allocation of Sh44 billion.
For private universities, he added, the funding requirement stands at Sh18 billion against an approved allocation of Sh3 billion.
The CS said there is a need to address the issue of bloated workforce in universities.
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