All Nippon Airways Co. and Japan Airlines Co. have canceled 309 and 264 flights, respectively.
Japan is being pounded by the strongest typhoon to hit the nation in 25 years, which made landfall on Tuesday with so much force that it smashed a huge tanker ship into a bridge.
As the typhoon lashed Shikoku and the Kii Peninsula, evacuation warnings and advisories were issued in many areas.
Tides in some areas were the highest since a typhoon in 1961, NHK said, with flooding covering one runway at Kansai airport near Osaka, forcing the closure of the airport and leaving about 3,000 tourists stranded.
"Customers connecting onto affected flights to Osaka will not be accepted at the original point of departure until further notice", the statement added.
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NHK also showed footage of a 100m-tall ferris wheel in Osaka turning furiously in the strong wind despite being switched off. Typhoon Cimarron sliced across western Japan less than two weeks ago, dumping heavy rain before heading out to sea.
Jebi has hit Japan with gusts as strong as 130 miles per hour, the Japan Meteorological Agency said.
West Japan Railway Co. has begun halting local trains and plans to stop all local services in the area's three main cities.
That made it a "very strong" typhoon, the second-highest on the JMA's scale.
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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.
More than 700 flights were cancelled.
It's now typhoon season in Japan which provides an annual tirade of extreme weather.
Warnings are in place from the Japan Meteorological Agency across most of Japan, with advisories in place elsewhere.
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. (JR West) halted operations on the Sanyo Shinkansen Line between Shin-Osaka and Hiroshima stations on the morning of September 4.
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Kyodo News reported Honda Motor Company halted operations at its Suzuka plant in Mie prefecture on Tuesday.