Typhoon Hagibis made landfall south of Tokyo on Saturday, moving north and bringing severe flooding.
Thirteen people are missing from the storm, public broadcaster NHK said.
In central Nagano prefecture, water surrounded Japan's famous bullet trains while helicopters plucked stranded residents from rooftops.
A total of 27,000 military troops and other rescue crews have been deployed in relief operations, the government said.
In Kawagoe city, north of Tokyo, emergency crews used boats to help residents trapped in a nursing home.