The agency added that if Jebi maintains its current strength of 216km per hour (135 mph) it will the first "strong typhoon" to strike Japan since 1993.
So far this summer, 200 people have been killed in Japan in July due to several typhoons and torrential rains.
Japanese media reported that flights to and from the region had been cancelled and some train service suspended.
JMA has also issued warnings of strong waves, floods, and landslides in Japan.
A police officer falls over in strong winds triggered by typhoon Jebi.
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Japan is bracing for flooding and landslides after what could be the strongest typhoon to hit the country in a quarter of a century made landfall on Tuesday.
The strongest typhoon to hit Japan in 25 years made landfall in southern Tokushima Prefecture on September 4, prompting evacuation warnings for hundreds of thousands of residents in the Kinki, Chugoku, Shikoku regions.
Tides in some areas were the highest since a typhoon in 1961, NHK public television said, with flooding covering the runways at Kansai International Airport in Osaka. Prime Minister Shinzo Abe canceled a scheduled trip to Kyushu, Japan's southernmost main island, to oversee the government's response to the typhoon, Kyodo said.
Jebi has a similar trajectory to Typhoon Cimaron which made landfall on 23 August, disrupting transport but causing limited damage and few injuries.
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He instructed his cabinet to "take all measures possible".
Television footage showed waves pounding the coastline, sheet metal tumbling across a parking lot and a truck turned on its side. In the city of Osaka, the Universal Studios Japan theme park and USA consulate both were closed. Many schools have been shut in the affected areas as well.
The flooding and landslides proved so deadly in part because many people did not heed evacuation warnings, which are not mandatory.
More than 175,000 people lost power in western Japan, according to the Ministry of Economy, Trade and Industry said, while more than a million people were advised to leave their homes by the Fire and Disaster Management Agency said.
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