He said Jebi may be extremely powerful when it makes landfall.
Local media reported two deaths in the storm, including a 71-year-old man killed in western Shiga prefecture after being trapped under a warehouse that collapsed in strong wind.
A police officer falls over in strong winds triggered by typhoon Jebi.
Evacuation advisories have been issued for more than 300,000 people in western Japan - including 280,000 in the port city of Kobe - with local officials setting up some 1,500 shelters, the central and local governments said in statements.
The typhoon first made landfall on the island of Shikoku and then again near Kobe on Honshu.
At least six people have reportedly died after Japan was hit by its strongest typhoon in 25 years.
Nationwide, the storm forced the cancelation of around 800 domestic and worldwide flights, while commercial facilities such as a popular theme park in Osaka and department stores were also closed.
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The NHK, Japan's national television channel, have said over 348 people were injured in the storm.
Kyodo News said Jebi was the strongest typhoon to make landfall since 1993, while NHK public television said tides in some areas were the highest since a typhoon in 1961. Another truck was almost blown off a bridge connecting Shikoku island and the main island of Honshu.
Railway services were canceled beforehand in the Kinki region, and many retail businesses announced that they would be closed on September 4.
Department stores and popular tourist attractions in western Japan, including Osaka and Kyoto prefectures, also fell victim to the typhoon, with many closing for the day.
ANA Holdings Inc. and Japan Airlines Co. canceled a total of 560 domestic and 13 worldwide flights, while Kansai global Airport closed its runways as the typhoon approached, local broadcaster NHK reported.
Prime Minister Shinzo Abe was forced to cancel a planned visit to southwestern prefectures on Tuesday.
Japan is now in its annual typhoon season, and is regularly struck by major storm systems during the summer and autumn. It was hit in July with lethal floods and landslides, leaving hundreds of people dead.
It has already left tens of thousands without power and authorities have urged people to move to safety.