Public broadcaster NHK said four people were missing due to landslides or floods, while at least 65 people were injured and more than 860 houses flooded.
The powerful typhoon hit at Toyohashi, Aichi prefecture, packing wind gusts of up to 162 kilometres per hour. It has been increasing in size and strength as it travelled over the Pacific.
Earlier in the day, the meteorological agency issued its highest alert for “possibly unprecedented heavy rain” in Kyoto and neighbouring prefectures, while Kyoto and other local authorities advised some 340,000 households to evacuate.
The tropical typhoon also hit the northeast, including the Fukushima area, bringing heavy rain to areas near the damaged nuclear plant run by Tokyo Electric Power (TEPCO).
About 350 domestic flights scheduled for September 16, a public holiday, were cancelled, mainly those departing from Tokyo. Transit official also reduced train service nationwide as a result of the tropical storm, NHK reported./.