Tropical storm Krosa is now tracking northeast, bringing torrential rains to northern Japan, through Saturday. Disaster officials are urging people to stay alert for landslides and flash flooding.
Large parts of the country experienced heavy rain and swelling rivers as Krosa made landfall in western Japan and proceeded northward.
The storm has left two people dead and at least 49 with injuries.
In Gifu city, four 20-person capacity tourist boats on the Nagara river were washed away or damaged. All tours were canceled on Friday. The river has overflowed as torrential rain fell upstream.
It is expected to change into a low-pressure system by early Saturday as it approaches Japan's northernmost prefecture of Hokkaido.
Up to 200 millimeters of rain is forecast in the 24-hour period through Saturday evening in Hokkaido.
The storm is disrupting transportation services in the area. Airlines and rail operators are advising passengers to check their websites for the latest information.