Gusts of up to 150 kilometres (93 miles) per hour have been recorded in western Japan, with coastal areas likely seeing even stronger winds, Japan's weather agency said.
With the agency warning of possible tornadoes in the western half of Japan, airlines grounded over 550 flights and a number of train services were suspended.
An 81-year-old man died in central Toyama prefecture when the wind blew over a shed, trapping him underneath, police said.
Forecasters said an expanding low pressure system in the Sea of Japan (East Sea) was forcing a cold front over the country, where it was bringing heavy rains and strong winds.
"This is like the core of a typhoon, but it is staying for a long time, whereas a typhoon usually moves rather quickly," a spokesman for the Japan Meteorological Agency said.
"Winds as strong as this are very rare," he said.
The meteorological agency said on its website the strong winds would move northwards into Wednesday, producing waves up to 10 metres (30 feet) high.
"In particular, ferocious winds are expected at sea (in the north) on the Sea of Japan side. Please be extremely wary of violent winds and high waves."
The agency also warned heavy rain could trigger landslides and flooding.
Japan Airlines cancelled 230 domestic and seven Asia-bound flights, affecting 31,600 passengers.
All Nippon Airways grounded 320 domestic flights, affecting 37,700 people.
East Japan Railways, which operates a vast train network in the eastern and northern regions, including Tokyo, cancelled some commuter lines and a number of long-distance services.
The nation's main bullet train, linking Tokyo and the western city of Osaka, was experiencing delays after a brief suspension, but was running as of early evening.
At least 97 people suffered injuries across the country, knocked over by sudden gusts or hit by flying debris, national broadcaster NHK said.
A number of trucks were toppled by the winds, creating localised traffic jams in Toyama prefecture.
NHK also reported a recently-constructed 10,000 ton tanker, which was moored off Ehime prefecture, had run aground.
Many companies sent employees home early. Canon told about 14,000 workers mostly in Tokyo and neighbouring Kanagawa prefecture to leave before the storm worsened.
"Most of them use public transportation to commute. The rain isn't so strong yet (in Tokyo) but the storm is likely to intensify and could disrupt train and other services," said company spokesman Hirotomo Fujimori, adding the early finish was to allow staff to get home.
Fujitsu permitted 25,000 employees in Tokyo and neighbouring prefectures to go home early if they wish, according to a company spokesman.