St Peters Kuna Mixed Secondary School in Migori County has been closed indefinitely after students went on rampage on Saturday over alleged mismanagement.
Rongo Sub-County Education director Charles Nyaribo on Saturday said the directive will create room for investigation and cool the tension.
"We have taken the decision to close the school indefinitely as we investigate the cause of the unrest. There is rising tension among the students and keeping them in school is risky," Mr Nyaribo said.
The students engaged police in running battles, damaging school property.
They accused Principal Rose Obondo of high-handedness and being insensitive to their needs.
"The principal wants every student to clear all the balances yet some of us come from poor backgrounds. The food we are served is very bad and some of us have consistently complained of stomach aches yet the principal does not address our issues," one of the students said.
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Another student said being chased from school due to lack of school fees is disrupting their preparations for the Kenya Certificate of Secondary Education examination.
"We are always on the road and rarely in class because of fees, yet we are supposed to be preparing for a national exam."
Further, Parent-Teacher Association chairman George Otieno said some staff have not been paid.
"Teachers employed by board of management have not been paid for months, students complain of poor meals yet we believe there is money in school. These are some of the possible reasons for the unrest," he said.
Mr Otieno said that those who instigated the unrest will be punished.
Tens of schools have also witnessed unrest such the burning of dormitories.