The East African nation has been battered by heavy rainfall since March, causing a trail of destruction and swamping entire villages.
"Some students whose schools were badly affected are going to nearby institutions," deputy government spokeswoman Mwanaisha Chidzuga told AFP.
Two thousand schools across the country have suffered varying degrees of damage, with some currently housing families displaced by floods, she said.
The reopening of schools was scheduled for April 29 after a three-week holiday and had been postponed twice due to damage to roads and some schools.
There are 35,570 primary schools and more than 10,000 secondary schools in Kenya, according to the ministry of education.
"Our officers are on the ground checking how many of the affected schools are able to continue with learning," Chidzuga said.
In a school in the capital Nairobi, teachers and students were contending with the aftermath of the flooding and forced to dry damp and mud-smudged books in the sun.
The torrential rains, amplified by the El Nino weather pattern, have killed at least 277 people in flood-related disasters since March, according to government data.
More than 290,000 people have been uprooted from their homes and 75 reported missing, raising fears that the toll could rise further.
Authorities on Monday warned against unnecessary travel and urged caution with more rains forecast.
"Flooding is expected in low lying areas, riparian areas and urban areas while landslides or mudslides may occur in areas with steep slopes, escarpments and ravines," the interior ministry said in an advisory.
Lake Victoria in western Kenya -- the largest in Africa -- and Lake Baringo in the Rift Valley were projected to continue overflowing and contribute to flooding, it added.
At least 53 cases of cholera have been reported, according to the health ministry.
Over 300 people died in rains and floods in Ethiopia, Kenya and Somalia late last year, just as the region was trying to recover from its worst drought in four decades that left millions of people hungry.
More than 500 people have died in the current monsoon in Kenya, Tanzania, Burundi, Rwanda, Uganda, Ethiopia and Somalia, according to government data and figures from the UN humanitarian agency, OCHA, compiled by AFP.
Kenyan President William Ruto, who has positioned himself at the forefront of African efforts to combat climate change, has blamed the region's calamitous cycle of drought and floods on a failure to protect the environment.