At least 29 schools have been closed and 31 served with closure notices following Education Cabinet Secretary George Magoha's directive.
The closer targets public and private schools found to be unsafe for learners.
The directive followed the death of eight students at Precious Talents School, Nairobi, when their classrooms collapsed last month.
West Pokot County Director of Education Jacob Onyiego (pictured) said most of the schools that had been closed had poor infrastructure and were not registered.
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"Some of the closed schools had cracks on the walls; some didn't have toilets; some boarding schools had unsafe dormitories and their kitchens were too dirty," he said.
In total, 15 private and 14 public schools were shut down; 26 were primary schools and three secondary schools.
Speaking to The Standard, Onyiego said more than 2,000 affected learners have been transferred to other schools.
"Some churches had been turned into schools. In some cases, communities started schools but did not register them," he said.
Some of the closed schools had unregistered teachers.
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Others had long-running land ownership wrangles which affected learning.
"West Pokot County is vast and many residents do not have tittle deeds. Some schools were built on private property and their administrations have been tussling with individuals over land," said Onyiego.