Typhoon Chaba is on course to make landfall in Hokuriku or Tohoku overnight on Wednesday, the weather agency has said.
The Japan Meteorological Agency warned of stormy conditions across much of eastern and western Japan, citing a risk of flooding along rivers and landslides in upland areas.
It said residents should brace for heavy rain at a rate of up to 50 mm per hour.
Chaba will be the seventh typhoon to strike Japan this year and the 18th in the region. It is gradually weakening.
Airlines canceled more than 140 flights. All Nippon Airways canceled 73 flights and Japan Airlines 33, affecting around 8,100 passengers in total. Fliers with tickets for Japan Air Commuter Co. and Skymark Airlines flights were also facing cancellations.
As of 1 p.m. the typhoon was centered in the Sea of Japan approximately 160 km north of Tsushima in Nagasaki Prefecture, moving northeast at a speed of 50 kph. It was packing winds of up to 180 kph, with an atmospheric pressure of 970 hectopascals at its center.
