The dire situation is blamed on total crop failure and last year’s politics.
He spoke to the media in Kabarnet town yesterday.
Cheptarus urged teachers to assist leaders and parents in mobilising children to resume school.
A spot check by the Star along the Kerio Valley in Baringo North on Monday revealed poverty, hunger and water shortage.
Some children from more than 30 schools in the county are yet to resume schools this term.
The majority are at home assisting their parents with household chores, herding livestock and trekking for long distances in searching of water.
Resident Reuben Aengwo, a parent at Cheptigit Primary School said half of the pupils have not gone to school.
“At one time the school had a class eight stream, but due to harsh drought conditions, pupils dropped out.
Rains failed from last July.
He appealed to the state to start a school feeding programme to attract children in the arid and semi-arid areas back in school.