The eye of Typhoon Hagibis made landfall shortly before 19:00 local time (10:00 GMT), in Izu Peninsula, south-west of Tokyo.
It is now moving up the eastern coast of Japan’s main island, with wind speeds of 225km/h (140mph).
More than 270,000 homes have lost power, Japanese outlet NHK reports.
Two people are said to have died, one a man whose vehicle flipped over in high winds in Chiba prefecture, east of Tokyo. The second was washed away in their car, local reports said.