More than 200 secondary schools are yet to receive government funds, a few weeks to the end of the first term, because of failing to register learners on the National Education Management Information System (Nemis).
Kenya Secondary Schools Heads Association (Kessha) chairman Kahi Indimuli said it is unfair for the Education ministry to expect learning to go on smoothly without adequate funding.
"These are more than 200,000 students with no funding, yet principals are required to provide essential services to them," Mr Indimuli lamented.
A week ago, Education Principal Secretary Belio Kipsang assured the affected schools that money would be released, but nothing has happened.
The government pays Sh22,244 annually for every secondary school student.
The money is disbursed in phases, with 50 percent sent in the first term, 30 percent in the second and the remaining in third.
Mr Indimuli said the most affected are day schools. "Principals need to pay non-teaching staff, teachers employed by boards of management as well as buy food for the students. They are unable to do that for now," he said.
Some 2.4 million students in secondary schools have been registered in Nemis, out of 2.8 million. Last month, the government released Sh36 billion to public primary and secondary schools.