Typhoon Talim is scheduled to make landfall in the Japanese island of Kyushu on Sunday, the weather agency announced on Saturday.
As of Saturday afternoon, Talim, the season's 18th typhoon in the Pacific, was at 480 km southwest of Kagoshima city, according to the Japan Meteorological Agency (JMA).
The storm, classified as "strong", was moving slowly toward the northeast with winds of up to 144 kph and an atmospheric pressure of 955 millibars near its centre, reports Efe news.
On Friday, the typhoon was classified as "very strong", and had caused heavy rainfall in the nearby islands.
Miyazaki city in Kyushu has recorded 360 mm of rainfall in the last 24 hours, with the airport being severely affected, receiving 71 mm of rain an hour, according to public broadcaster NHK.
The JMA has predicted the Pacific region will receive around 50 mm of rainfall per hour on Saturday, which could increase to 80 mm in certain regions on Sunday.
The agency also released warning on risks of landslide.
Talim originated in the coasts of the Philippines on September 9, and led to an evacuation of half a million people in Taiwan and China ahead of its arrival and before the storm changed direction toward Japan.