Emirates said on Tuesday that all flights in and out of Osaka Kansai International Airport have been cancelled until Thursday at the earliest after the strongest typhoon to hit Japan in 25 years made landfall.
More than a million people have been urged to evacuate as the storm battered the country's west with violent winds and heavy rainfall.
Typhoon Jebi, with winds of up to 216 kilometres (135 miles) per hour, swept a tanker anchored in Osaka Bay into a bridge and partially flooded Kansai International Airport on an island in the bay.
An Emirates spokesperson said: “Customers are advised that due to Typhoon Jebi, all flights into/out of Osaka Kansai International Airport on 4 and 5 September have been cancelled due to the airport closure and heavy flooding.
"Customers connecting onto affected flights to Osaka will not be accepted at the original point of departure until further notice. Passengers who have already started their journey and are enroute will be offered re-route options to Haneda and Narita airports subject to availability."
Emirates added that customers booked to travel to/from Osaka can opt to change their flights and postpone their departure up to 7 days later than originally booked and are requested to contact their travel agent or booking offices to make changes to their bookings.
"The situation is being closely monitored. We apologize for any inconvenience,” the airline said in a statement.
The severe weather has left tens of thousands without power and forced the cancellation of hundreds of flights as well as trains and ferries.
Prime Minister Shinzo Abe urged people to evacuate early and ordered his government to take all necessary measures to protect residents.
Japan's weather agency warned of possible landslides, flooding and violent winds, as well as high tides, lightning and tornadoes in a swathe of the Japanese archipelago.
Arriving on land, Jebi had winds of up to 162 kilometres (100 miles) per hour at its centre, making it a "very strong" typhoon, the weather agency's chief forecaster Ryuta Kurora told AFP.
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.
Local media warned that the wind was strong enough to topple traditional-style wooden houses as well as power poles, and urged people in affected areas to avoid non-essential travel.
Television footage showed high waves crashing into breakers and flying debris in areas where the storm made landfall.
Primary and middle schools in affected areas 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, including several international flights departing and arriving at Nagoya and Osaka, along with ferries, local train services and some bullet train lines.
More than 175,000 buildings in central and western Japan were without power, according to a tally compiled by Bloomberg News of local utilities.
Jebi has a similar trajectory to Typhoon Cimaron which made landfall on August 23, disrupting transport but causing limited damage and few injuries.
Japan is regularly struck by major storms during the summer and autumn.
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