Heavy snow is expected in the Kanto plain region that includes Tokyo, with central Tokyo and the nearby Yokohama covered with snow as of 8 am (6am Thai time).
Through Sunday morning, as much as 50 centimetres of snow is expected in the Kanto-Koshin area and 40cm in extended areas from western to eastern Japan, according to the agency.
A number of domestic flights to and from Tokyo's Haneda airport have been cancelled, while the bullet trains operating in western Japan are expected to fall behind schedule, the operators said.
Some sections of expressways were also closed due to the snow.
In Tokyo, several universities delayed the starting times of their entrance examinations for the new academic that begins in April.