Tropical storm Krosa is now tracking North, bringing torrential rains to northern Japan, through Saturday.
Heavy rains lashed large parts of the country and rivers swelled as Krosa approached.
In Gifu city, tour boats on the Nagara river were damaged and some swept away.
The storm has disrupted transport 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 3 p.m. on Friday, Krosa was 340 kilometers west-southwest of Okushiri Island in the Sea of Japan.
It's expected to change into a low-pressure system by early Saturday.
Up to 250 millimeters of rain is forecast in the 24-hour period through noon on Saturday in Hokkaido and 150 millimeters in the Tohoku region.
The storm has so far left two people dead and at least 49 injured.