Farms and homes in Miyazaki on the southern main island of Kyushu were flooded as Typhoon Trami swept across southwestern Japan.
The island's main carrier, China Air Lines (CAL), was canceling Sunday's flights CI156/157 and CI172/173 between Taiwan Taoyuan International Airport and Kansai, flights CI166/167 between Kaohsiung and Kansai, and flights 178/179 between Taoyuan and Takamatsu, according to the Apple Daily.
Trami is now heading towards Japan's northeast.
National broadcaster NHK reported that one man had died in Tottori prefecture on Honshu island and another was missing on the southern island of Kyushu.
There have been more than 900 flight cancellations announced by various airlines on Sunday, affecting more than 70,000 passengers, Kyodo reported.
After pummelling Japan's outlying islands including Okinawa, the storm made landfall south of the city of Osaka in the western part of the country around 8:00 pm local time (1100 GMT).
Bullet trains running between the two western Japan cities of Osaka and Hiroshima will suspend operations Sunday morning in anticipation of heavy rain and wind, operator West Japan Railway said on Saturday.
Trami follows on the heels of several large typhoons to hit major Asian population centres this month, including Jebi, which forced the closure of Kansai International Airport.
In Amami, Kagoshima Prefecture, an 11-meter-high lighthouse at a Naze Port pier was apparently knocked down and washed away into the sea by strong winds and high waves, according to the Amami Coast Guard Office.
West Japan Railway Co. said all trains in the area covering Kyoto, Osaka and Kobe would suspend operations from about noon September 30 as the typhoon approaches the Kansai region.
It's the strongest typhoon to make landfall in Japan in 25 years. The airport only fully reopened on Sept 21.
East Japan Railway Co. shut down all of its train services in the Tokyo Metropolitan area around 8 p.m.
Western regions are still recovering from the most powerful typhoon to strike the country in a quarter of a century in early September. More than 80 people were injured, it also said.
Trami will threaten lives and property as it slams the Ryukyu Islands and mainland Japan with destructive winds, flooding rain and an inundating storm surge.
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