Footage on national broadcaster NHK showed homes with roofs partly sheared off, while cars drove wheels-deep on flooded roads in the country's southwest.
The storm made landfall in Kyushu on Thursday, bringing record levels of rainfall.
One person was missing and more than 100 have been injured, Japan's Fire and Disaster Management Agency said.
More than 35,000 homes were without power in southern Kyushu's Kagoshima prefecture, according to Kyushu Electric.
Shanshan, centred in the Pacific Ocean some 480km southwest of Tokyo at 12:50pm on Saturday, triggered heavy rain as far away as the northernmost prefecture of Hokkaido, despite being downgraded to a tropical storm on Friday. Winds were gusting up to 90kmh.
Authorities have issued flood and landslide warnings around the country since the storm's arrival, halting air and rail services and shutting factories.
The storm is forecast to weaken to a tropical depression over the weekend but is expected to continue to bring heavy rain, NHK reported.
