Some stores in Osaka and Kyoto prefectures as well as in other parts of western Japan have shut down operations for the day, as did the Universal Studios theme park in Osaka.
Due to the typhoon on Tuesday, the airport's runway and the basement floor of a terminal building were flooded, and all of its runway and taxiway areas were closed.
Japan was lashed by heavy winds, rain, and waves after Typhoon Jebi made landfall.
Typhoon Jebi landed with "very strong" force in Tokushima prefecture in the early afternoon, the strongest typhoon to hit the country's mainland since 1993, said Akihiro Kikuchi, from Japan's Meteorological Agency.
The typhoon is expected to cross the main island of Honshu and reach the Sea of Japan by the night of September 4.
As of 10pm local time, Jebi was traveling north-northeast over the Sea of Japan north of Niigata Prefecture at a speed of 70 kilometers per hour and with an atmospheric pressure of 975 hectopascals at its centre.
A 2,591-ton tanker crashes into a bridge connecting Kansai airport, which is built on a man-made island in a bay, to the mainland, in Izumisano, western Japan, in this photo taken by Kyodo September 4, 2018.
High waves hit breakwaters at a port of Aki, Kochi prefecture, Japan, on Tuesday.
Jebi is predicted to bring heavy rains tomorrow.
About 1.45 million households were without power in Osaka and its surrounding areas at 3pm local time.
Video captured in Kyoto shows the glass ceiling of Kyoto Station breaking or partially collapsing, sending chunks of glass falling toward commuters below.
PAL said it would inform passengers of further updates on the status of the regular flights and possible replacement flights that were canceled today.
Powerful winds overturned vehicles and caused widespread damage in Osaka, one of Japan's largest cities. Toyota Motor Corp said it was cancelling the night shift at 14 plants.
Tokyo escaped relatively unscathed, with some intermittent squalls.
Prime Minister Shinzo Abe canceled a scheduled trip to Kyushu, Japan's southernmost main island, to oversee the government's response to the typhoon, said Chief Cabinet Secretary Yoshihide Suga.