Packing winds of up to 180 kilometres (112 miles) per hour, the typhoon made landfall in central Aichi prefecture at around 7:00 pm (1000 GMT) and was moving up the main island of Honshu, the Japan Meteorological Agency said.
A 29-year-old man was swept away by high waves when Jelawat hit Okinawa and was later confirmed dead, while at least 140 people were injured in eight prefectures, according to public broadcaster NHK.
The typhoon is forecast to churn northeastwards towards Tokyo over the next 24 hours and bring torrential rainfall and towering waves up to 10 metres (33 feet) high.
More than 500 flights, mainly in western Japan, were cancelled on Sunday and some shinkansen bullet train services across the country had been suspended, Kyodo said.
Local authorities have ordered more than 2,000 in central Mie to evacuate, while tens of thousands of people were advised to leave home for safe shelter, according to NHK.
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Edited By Cen Fox Post Team
