Khanun could make landfall on the southwestern main island of Kyushu, some 858 km (533 miles) from Tokyo, on Thursday, but areas of the region have already been inundated with a whole month's worth on rainfall in the past week, the Japan Meteorological Agency (JMA) said.
The storm is currently in the sea south of Kyushu after wreaking havoc in the southwestern Okinawa region.
It is maintaining its strength and moving at an unusually slow 10 kph (6 mph), meaning the wind and rain will linger for longer.
The JMA issued heavy rain and high wind warnings to many parts of southern and western Japan. Railway operator West Japan Railway Co has also suspended some of its Shinkansen bullet train service in Kyushu.
A second storm, Lan, had formed in the Pacific Ocean south of Japan and was predicted to strengthen as it heads north, possibly affecting Tokyo early next week, JMA said.
The two storms arrive at the start of Obon, the peak summer holiday season when many Japanese leave big cities for their ancestral hometowns.
(Reporting by Mariko Katsumura and Elaine Lies; editing by Miral Fahmy)
