Kyodo News reported the storm that raked much of the country Tuesday night into Wednesday disrupted sea and rail transportation in addition to forcing the cancellation of more than 700 domestic flights.
Besides the fatalities -- which included a Toyama man in his 80s who was crushed by a building that was knocked down -- several people were injured, Kyodo said.
A 48-year-old man sustained broken bones in Kariya when a section of baseball field fence hit him.
An elderly woman in Tsuruga was hurt when high winds knocked her to the ground as she stepped outside her home, Kyodo said.
Winds as strong as 85 mph were recorded at Mount Aso.