The latest typhoon, the 24th this season, made landfall in western Japan at around 8 p.m., and began to move towards the capital around midnight, bringing rain and strong winds, reports Efe news.
It was, however, sunny in Tokyo on Monday morning as the typhoon had already moved to the northeast of Japan towards the Pacific at a 95 km/h speed, packing winds of up to 126 km/h and gusts of up to 180 km/h.
According to local media, a truck driver was killed by a landslide in the western town of Tottori while another man appeared to have drowned in a river in Yamanashi, west of Tokyo.
A 60-year-old woman is missing after she was dragged into an irrigation canal in Miyazaki, in the southwest of the country.
More than a thousand flights were canceled because of the typhoon nationwide, and another 230 flights were called off on Monday, according to national broadcaster NHK.
The Kansai international airport in Osaka, the third busiest airport in Japan, stopped its services on Sunday and resumed on Monday.
The NHK reported that around 410,000 houses in Tokyo and nearby areas were left without power supply due to network damages.
Train services were also suspended in different parts of the country as well as in the outskirts of Tokyo but were resumed on Monday morning.