Powerful Typhoon Jelawat left at least two people dead and more than 180 injured in Japan over the weekend before passing out into the Pacific on Monday, the weather agency and local media said.
The typhoon, packing winds of up to 126 kilometres (78 miles) per hour, was northeast of Nemuro in eastern Hokkaido over the Pacific at 0200 GMT, the Japan Meteorological Agency said.
A 56-year-old man was confirmed to have drowned in Mie, central Japan, after going missing on Sunday, local officials said.
A 29-year-old man was swept to his death by high waves when Jelawat hit the southern island of Okinawa on Sunday, public broadcaster NHK reported.
NHK also reported that at least 181 people were injured in typhoon-related incidents across the nation.
On Sunday, several local governments issued evacuation advisories for tens of thousands of residents because of the fear of flooding caused by rising river levels.
The typhoon is expected to be downgraded to a tropical depression later in the day, but the meteorological agency warned there would be further strong winds and high waves in Hokkaido.
More than 500 flights, mainly in western Japan, were cancelled on Sunday and some shinkansen bullet train services across the country were suspended, news reports said.