Typhoon Melor on Thursday became the first tropical cyclone to hit Japan in two years, killing two people and injuring 56. Hundreds of flights were cancelled and schools in Osaka and Tokyo closed.
After making landfall near Chita peninsula in Aichi prefecture shortly after 5 am, the typhoon moved northeast at a speed of 50 km per hour, according to the Japan Meteorological Agency.
The agency has issued warnings against strong winds, heavy rain and tidal waves.
A 54-year-old man died after his motorbike hit a tree felled by the typhoon in Minabe, Wakayama prefecture, and a 69-year-old man died when a broken branch hit him at a shrine in Fujimi, Saitama prefecture, media reports.
According to Kyodo News, up to 56 people in 15 prefectures were injured till noon.
More than 440 domestic and international flights were cancelled, and up to 18 bullet-train services were suspended.
In Osaka city, all 434 municipality run elementary and junior high schools were closed, while 396 public elementary and junior high schools were closed in Tokyo.