A powerful typhoon, the 18th of this season, made landfall in Japan's Kagoshima prefecture on Sunday, the weather agency said.
Typhoon Talim, with central atmospheric pressure at 975 hectopascals, had winds at a speed of 30 metres per second near its centre, with gusts reaching nearly 45 meters per second, reports Xinhua news agency.
Heavy rain battered wide swathe of southwestern Japan and the weather agency warned about possible mudslides, violent winds and high waves.
More than 640 flights have been cancelled due to the typhoon, and train operations, including part of the Shinkansen bullet train services in Kyushu, were suspended.
Some 1,400 households in Kagoshima prefecture and 600 households in Miyazaki prefecture suffered power failure.
As of 11 a.m., hundreds of thousands of people in Miyazaki, Kagoshima, Oita, Kumamoto and Fukuoka prefectures have been advised to evacuate.