Evacuation advisories were issued for 1.19 million people in western and central Japan, with another 16,000 people issued with stronger but non-mandatory evacuation orders, the fire and disaster management agency said.
The bridge that links the island airport with the mainland was hit by a storm-driven tanker ship Tuesday, shearing off one chunk and dislodging a section of roadway from the rest of the bridge.
The weather agency said the typhoon is expected to travel to an area west of Hokkaido and weaken to an extratropical cyclone by Wednesday noon.
The typhoon bore down on western Japan on Tuesday, cancelling more than 600 flights according to Japanese broadcaster NHK.
Weather forecaster Ryuta Kurora described the typhoon as "very strong", adding: "This is (the strongest) since 1993".
Scaffolding of a building being demolished, collapse, following a powerful typhoon in Osaka, western Japan, Tuesday, Sep 4, 2018.
Wind gusts of up to 166 km/h were recorded in one part of Shikoku, with forecasts for gusts as high as 216km/h.
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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.
Some parts are likely to see up to 300mm of rain fall in a 24 hour period with winds gusting up to 216 kilometres per hour.
In the hard-hit city of Osaka, high seas poured into Kansai International Airport, flooding one of its two runways and cargo storage and other facilities, forcing the airport to shut down, said the Ministry of Land, Infrastructure, Transport and Tourism.
Shinkansen bullet train services between Tokyo and Hiroshima were suspended and Universal Studios Japan was closed.
A police auto makes through a flooded road following a powerful typhoon in Osaka, western Japan, Tuesday, Sep 4, 2018.
Toyota Motor Corp. halted operations at most of its group plants, and Honda Motor Co. stopped its Suzuka plant in Mie prefecture.
Tokyo escaped relatively unscathed, with some intermittent squalls.