The Japan Meteorological Agency said a wide area of Japan should be on high alert for strong winds, high waves and heavy downpours.
Jebi - whose name means "swallow" in Korean - is the latest harsh weather to hit Japan this summer following deadly rains, landslides, floods and record-breaking heat that killed hundreds of people. Authorities warn that when it makes landfall later in the day, it could be the strongest storm to do so in Japan in a quarter century.
Jebi, the 21st typhoon of the season, made landfall in Tokushima prefecture on Japan's smallest main island of Shikoku, and is on path to strike the part of the country home to Osaka, Kyoto and Kobe.
By the time the typhoon makes landfall, it's sustained winds are forecast to be around winds are 170kmph with gusts nearer to 200kmph.
Evacuation advisories were issued for more than 1 million people as the wind and rain began picking up, the Fire and Disaster Management Agency said.
Television footage showed waves pounding the coastline amid warnings of high tides later in the day.
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Around 87mm (3.4 inches) of rain had drenched some areas in an hour on Tuesday morning.
The agency's chief forecaster, Ryuta Kurora, told a news conference on Monday that Typhoon Jebi is stronger than the storm that struck western Japan last month.
Primary and middle schools in affected areas are closed for safety reasons, while regional businesses also reacted quickly, with a major railway firm and Universal Studios Japan in Osaka shutting down for Tuesday.
More than 700 flights were cancelled, including several global flights departing and arriving at Nagoya and Osaka, along with ferries, local train services and some bullet train lines. However, the ground remains saturated and many parts of Honshu remain flooded. Toyota Motor Corp said it was cancelling the night shift at 14 plants.
It's possible it may end up close to the parts of Japan where more than 200 people were killed in heavy rains and flooding in July. However, it is set to speed up once it makes landfall, minimising the amount of rain that will fall in one place.