The agency issued a heavy snow warning for Tokyo, the first such warning for the capital in 13 years, calling on residents not to go out unless necessary.
Japan Airlines cancelled 265 domestic flights on Saturday due to heavy snow, public broadcaster NHK said.
All Nippon Airways separately cancelled 33 flights, a company spokesman said, adding that more cancellations were expected Saturday afternoon.
Airports in the western cities of Hiroshima and Kagawa were closed as operators were removing snow from the runways.
Railway operators temporarily suspended services of Shinkansen bullet trains in western Japan, NHK said.
Some sections of expressways in central Japan were also closed due to the snow, Kyodo News said.
In Tokyo, several universities delayed the starting times of their entrance examinations for the new academic year that begins in April, Kyodo added.