Waist-high floods in some areas left rescuers scrambling to pluck people to safety as a wide area was deluged in the wake of Typhoon Etau.
Typhoon Etau, which smashed into Japan on Wednesday, moved out into the Sea of Japan by the end of the day, but a wall of rain continued to lash the country.
"This is a scale of downpour that we have not experienced before. Grave danger could be imminent," forecaster Takuya Deshimaru told an emergency press conference.