Weather officials have issued an emergency warning for violent winds, high waves and a storm surge for Kagoshima Prefecture in the southwest of the country.
The eye of Typhoon Nanmadol is clearly visible in satellite images. The typhoon has developed rapidly since Friday night.
It is south of Japan and moving slowly north-north-west on Saturday night. It has come close to the Daito Islands of Okinawa Prefecture. It is expected to come very near the Amami Islands and the southwestern main island of Kyushu on Sunday through Monday.
Officials say maximum winds of up to 198 kilometers per hour will lash the region, with peak gusts reaching 270 kilometers per hour through Sunday.
Southern Kyushu could get as much as 500 millimeters of rain in the 24-hour period through Sunday evening. The agency also warns that as the typhoon is large, rain and winds could intensify even in areas far from it, and that its effects could be prolonged.
Flights have been disrupted at airports around the country.
As of 8:30 p.m., Japan Airlines and All Nippon Airways had canceled over 120 flights for the day. Another 504 were canceled for Sunday. Other airlines are also canceling services.
The Japan Railways Group says some bullet train services may be suspended on Sunday and Monday.
As of 8:30 p.m., the operator of the Kyushu Shinkansen said it would suspend service between Kumamoto and Kagoshima Chuo all day on Sunday. It said it will suspend service between Hakata and Kumamoto from around noon.
The typhoon is forecast to head northeast and travel across Japan's main island of Honshu, to eastern and northern Japan through Tuesday. Winds may intensify even away from the typhoon's center.