Two people are dead and at least 126 others injured as the powerful typhoon rips through the country. Jebi is one of the strongest typhoons to make landfall in Japan in 25 years.
One of Japan's key airports, Kansai International Airport, is completely shut down because of flooding.
Transport Ministry officials say several planes were submerged up to their engines.
They say it's not clear when airport operations will start up again.
Strong winds in the same area rammed a fuel tanker into the bridge linking the airport to the city of Izumisano in Osaka.
Rescue operations are underway for 11 crew members.
No one was hurt in the crash. The crew cannot start the engine and officials are waiting for the weather to improve to tug the vessel.
The bridge's closure has cut off road and rail links, leaving people stuck at the airport.
An airport hotel is letting people use its ballroom as a temporary shelter.
The wind in Osaka was so powerful that rooftops blew away and trucks toppled. The strong wind turned a Ferris wheel at a popular aquarium.
Evacuation advisories remain in place in many parts of western and central Japan. Officials are warning that heavy rain could lead to landslides or flooding.
There have also been major disruptions to transportation links.
The Shinkansen bullet train service between Tokyo and Okayama is suspended.
Airline companies have cancelled hundreds of domestic flights scheduled for Tuesday mainly in western Japan.