Typhoon Francisco was expected to make landfall in Kyushu on Tuesday, the Meteorological Agency said.
The agency warned of potential flooding, mudslides and high waves in the region as the season's eighth typhoon was expected to bring strong winds and torrential rain.
Shikoku was also expected to see rough weather.
A number of flights to and from airports in Kyushu were expected to be canceled throughout Tuesday.
As of 8 p.m. Monday, the typhoon was traveling some 170 kilometers south-southeast of Cape Ashizuri in Kochi Prefecture at a speed of 20 kilometers per hour with an atmospheric pressure of 975 hectopascals at its center and packing winds of up to 180 kph, the Meteorological Agency said.
Kyushu may see up to 300 millimeters of rainfall in the 24-hour period to 6 p.m. Tuesday while as much as 250 mm is expected in Shikoku, the agency said.
Through Tuesday, winds of up to 180 kph and waves as high as 9 meters are forecast for southern Kyushu, the agency said. Northern Kyushu and Shikoku could be hit with winds of up to 126 kph and 7-meter waves, it said.
Rain is likely to continue in western Japan regions on the Pacific side even after the typhoon passes as moist air is forecast to continue flowing into the areas.