The Commission for University Education has introduced a quality control charge for every student, a move that will see an increase in fees.
In a circular to public and private universities, CUE said it would start charging the fee annually to finance quality control measures.
According to the mid-December circular, undergraduates will pay Sh1,000, masters’ students Sh1,500 and PhD Sh2,000 a year from the 2015/16 academic year.
Postgraduate diploma students will be required to pay Sh800 every year.
Kenya has 70 universities, 38 of them private and 32 public. The student population is 485,000.
The charges come at a time vice-chancellors of public universities are pushing for fees being pegged on degree programmes.
If the VCs have their way, annual fee for some courses like medicine and engineering could be as high as Sh500,000.
Should the fee increase be approved, the number of students sponsored by the government could reduce and the learners made to pay the balance.
In the current system, the government allocates Sh120,000 annually per student despite some programmes being more costly than others.
However, the CUE circular did not indicate if students pursuing diploma and certificate courses would pay the new fee.
While presiding over the eleventh graduation ceremony of Kabarak University on Friday, CUE Chairman Henry Thairu said some institutions faced closure for failing to meet the minimum requirements to operate.
He said CUE was finalising vetting that would see the colleges, some of them private, shut down.
“We must safeguard the integrity of higher learning. From next year, it will not be business as usual,” said Prof Thairu.
He said every university would be made to collect and remit the quality control fees.
St Paul’s University Vice-Chancellor Joseph Galgalo said his institution had begun negotiations with the commission to see if the new charges could be reduced or withdrawn altogether.