The 14th typhoon of the season, classified as a super typhoon by the U.S. Navy's Joint Typhoon Warning Center, could bring record rainfall, the JMA said, warning of the risk of rivers overflowing and landslides.
Southern Kyushu could receive 500 mm (20 inches) of rain and wind gusts of up to 250 km per hour (155 miles per hour) on Sunday, while the central Tokai region could see 300 mm (12 inches) of rain, the agency forecast.
Railway operators have cancelled trains in the region with convenience store chain Seven-Eleven Japan temporarily shutting around 950 stores.
The storm is forecast to curve east and pass over Japan's main island of Honshu early next week before moving out to sea by Wednesday.
(Reporting by Sam Nussey, Maki Shiraki and Ritsuko Shimizu; Editing by Christian Schmollinger)
