Severe tropical storm Mitag is moving northward over the East China Sea and is expected to approach the Korean Peninsula.
Humid air from the storm will cause heavy localized rains accompanied by lightning in the northern Kyushu and Shikoku regions through Thursday.
The Meteorological Agency is warning of mudslides and flooding in low-lying areas.
Over the next 24 hours until Thursday morning, up to 150 millimeters of rain will fall in northern Kyushu and Shikoku, and 120 millimeters in southern Kyushu.
During the 24-hour period to Friday morning, the Shikoku region will see 100 to 200 millimeters of rain.
Weather officials say northern Kyushu and its surrounding areas will experience extremely strong winds early Thursday. They forecast maximum winds of 72 kilometers per hour, with gusts of up to 108 kilometers per hour. Waves will be as high as five meters.