A tanker anchored in Osaka Bay was swept into a bridge and Kansai worldwide airport was partially flooded by high waves whipped up by the storm.
Bracing for Jebi, domestic airlines have played it safe, canceling a number of local and global flights mainly scheduled to depart and arrive in airports in western and central Japan.
A photo circulating on social media shows flooding at Osaka's Kansai International Airport as Typhoon Jebi battered Japan's western coast on Sep 4, 2018.
Almost 600 domestic and global flights were cancelled, along with scores of ferries and trains, the public broadcaster NHK said.
Wind gusts of up to 166 km/h (103 mph) were recorded in one part of Shikoku, with forecasts for gusts as high as 216 km/h (135 mph).
Japan's weather agency has issued warnings about possible landslides, flooding and violent winds, as well as high tides, lightning and tornadoes in a swath of western Japan including the major cities of Osaka and Kyoto.
Typhoon Jebi is believed to be the strongest tropical cyclone to come ashore in Japan in 25 years. "It is possible that (Jebi) will make landfall while maintaining its extreme strength", said Ryuta Kurora, the agency's chief forecaster.
ANA Holdings said it was cancelling 247 domestic and 8 worldwide flights, while Japan Airlines pulled 176 domestic flights.
Primary and middle schools in the storm's path were closed while regional businesses also reacted quickly, with Universal Studios Japan in Osaka shutting down for Tuesday along with factories for several large manufacturers. Shinkansen high-speed trains between Osaka and Hiroshima were canceled from mid-morning, with the operator warning it might not be able to restart services for the rest of the day.
Toyota Motor Corp. said it will suspend its nighttime operations at 14 plants across the nation, including in Aichi, Fukuoka and Miyagi prefectures.
Some of the areas affected are still recovering from devastating record rains that killed at least 200 people over the summer.
Japanese Prime Minister Shinzo Abe, who has been campaigning across the country ahead of the ruling Liberal Democratic Party's leadership election later this month, cancelled his trip to Kyushu region to take stock of the situation.