In Kanagawa, west of Tokyo, floodwaters stalled traffic and blocked roads.
The storm, which made landfall as a powerful typhoon, has weakened but continues to drench the region.
Several planes aborted their landings and ascended back into the air at Fukuoka Airport on Thursday, due to the severe weather conditions.
The Japan Meteorological Agency has issued warnings for potential landslides and forecasts up to 30 cm of rainfall in some areas, with disruptions to transport and business continuing across the country.
