Education CS George Magoha asked VCs to lay ground for the drastic measures.
The VCs are expected to come up with the number of academic or non- academic staff to be laid off, the programmes to be merged and campuses to be closed.
The decision is a blow to more than 27,000 staff in public universities, among them 9,000 lecturers.
The Education ministry has given universities two weeks to prepare a list of the institutions to be merged and those to be shut down.
At a meeting with vice-chancellors and finance officers of the 31 chartered public universities and seven university colleges, Education Secretary George Magoha asked the administrators to lay ground for the drastic measures.
The Commission for University Education (CUE) will also submit its report on the merger on July 31, which is different from what vice-chancellors are expected to draft.
At the Kenya Institute of Curriculum Development where the closed-door meeting took place yesterday, vice-chancellors protested the directive, saying it was being undertaken without involving all stakeholders.
The vice-chancellors are expected to come up with the number of academic or non- academic staff to be laid off, the programmes to be merged and campuses to be closed.
The decision is a blow to more than 27,000 staff in public universities, among them 9,000 lecturers. Some of the issues discussed at the closed-door meeting included pending bills, pension, taxes, debts and Sacco remittances.
Already the University of Nairobi has identified 20 programmes to be phased out.
The vice-chancellors also told the Education secretary that the new policy is coming from the top and not from universities which ought to have provided “critical mechanism” of the plan.
The Universities Academic Staff Union (Uasu) has joined the debate by opposing the plan.
“We need sobriety in this whole process or else we will mess up. We have to involve all stakeholders including politicians,” said a vice-chancellor who asked not to be named.
Vice-chancellors also complained that the government has been “talking to itself” in the whole process and wondered where students leaving secondary schools under 100 percent transition plan will go to.
During the meeting, Prof. Magoha ruled out any extra funding to the institutions saying they will have to use the Sh97 billion allocated to them.
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