Residential streets were flooded with muddy water from rivers, and swaths of homes lost power after Typhoon Nanmadol made landfall in the Kyushu region Sunday then weakened to a tropical storm.
Nanmadol was packing sustained winds of 108 kilometers per hour and gusts up to 162 kilometers per hour, according to the Japan Meteorological Agency.
Tens of thousands of people spent the night at gymnasiums and other facilities in a precautionary evacuation of vulnerable homes.
More than 60 people have been injured, including those who fell down in the rain or were hit by shards of glass, according to Japanese media reports.
Torrential winds smashed signboards. A construction crane snapped and a window at a pachinko parlor was shattered in the city of Kagoshima, southwestern Japan.
Bullet trains and airlines suspended service. Warnings were issued about landslides and swelling rivers. Convenience store chains and delivery services temporarily shuttered in southwestern Japan, while some highways were closed and people had some problems with cellphone connections.
The storm is forecast to continue its northeasterly path over Japan's main island of Honshu, unleashing heavy rainfall over the region that includes the cities of Osaka and Kyoto, before moving over Tokyo on Tuesday and then toward northeastern Japan.