Tropical storm Krosa is now tracking North, bringing torrential rains to northern Japan, through Saturday.
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.
The storm has disrupted transportation services during Japan's peak summer holiday period.
Airlines canceled about 50 domestic flights on Friday. A passenger said, "I was afraid that the plane wouldn't be able to land because the wind was so strong. I'm glad to be back home safely."
The Meteorological Agency says as of 6 p.m. on Friday, Krosa was 230 kilometers west of Okushiri Island in the Sea of Japan.
The storm 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 and 150 millimeters in the Tohoku region.
Hokkaido Railway Company has canceled more than 120 trains through Saturday.
Airlines have also canceled more than 10 domestic flights and are advising passengers to check online for the latest flight information.