Footage on national broadcaster NHK showed homes with roofs partly shorn off while cars drove wheels-deep on flooded roads in the country's southwest.
The storm crossed the coast in Kyushu on Thursday, bringing record levels of rainfall.
One person was missing and more than 100 had been injured, Japan's Fire and Disaster Management Agency said.
Typhoon Shanshan's arrival halted air and rail services and closed factories. (AP PHOTO)
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 after noon 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 90km/h.
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 was forecast to weaken to a tropical depression at the weekend but was expected to continue to bring heavy rain, NHK reported.
