The season's 21st typhoon in the Pacific region was packing wind speeds of 126 kilometers (77 miles) per hour and moving at a speed of 20 kilometers per hour after battering the southern island of Okinawa at the weekend, the agency said.
"The typhoon is expected to near or make landfall in western Japan on the morning of September 29, and then move through Japan's main island of Honshu," the agency said in the latest forecast on its website.
The agency said up to 200 millimeters of rainfall was expected to hit southern Kyushu within a 24 hour period.
Earlier this month, Typhoon Songda pounded many parts of Japan, leaving at least 45 people dead or missing.