Thousands of people were left stranded at one of the country’s main international airports after it was besieged by high winds and heavy rain, the Association Press reports.
Kansai International airport, which serves the country’s second city Osaka, remained shut on Wednesday morning due to severe flooding.
Elsewhere, traffic and travel links across much of western Japan have been affected by the storm.
Jebi, which has since been downgraded to a tropical storm, is understood to be the strongest typhoon to make landfall in Japan since 1993, according to the Japanese meteorological agency.
Reports in Japan suggest more than 10 people are understood to have died, with more than 300 injured. Hundreds of thousands are without power.
Efforts to evacuate Kansai International, which is situated on two artificial islands in Osaka Bay, were hampered not just by the weather, but by a ship that collided with a bridge connecting the airport with the mainland.
The Foreign Office updated its travel advice overnight to warn Britons of the disruption and what they should do if they are affected.
“Wide areas of western Japan are experiencing transport disruption in the wake of Typhoon Jebi,” said the FCO.
“Kansai International Airport (KIX) was closed and all flights cancelled on September 4. As of September 5, no plans to resume service have been announced.
“If you are planning to travel through the affected areas, or use the airport, you should follow the advice of local authorities, transportation services and check with your airlines.
“The Osaka Prefectural government is publishing up-to-date information and guidance on their website.”
Some Shinkansen (bullet train) services have also been affected.