Typhoon Trami made landfall on Sunday at 20:00 local time (11:00 GMT) near the western city of Osaka, with gusts of up to 216 km/h (134 mph).
The storm caused widespread disruption, with many flights and trains cancelled. More than 750,000 homes lost power.
At least 120 people were injured. The typhoon comes less than a month after the country's strongest storm in 25 years hit western Japan.
Typhoon Jebi caused widespread flooding and at least seven deaths in early September.