The Japan Meteorological Agency said the typhoon could possibly make landfall on the main islands Sunday afternoon, which would make Trami the fifth typhoon to hit the country's main islands since July.
Outlying islands in the Okinawan chain, some 1,000 km southwest of Tokyo, were being pounded by heavy rain and high tides a day before an Okinawan gubernatorial election on Sunday.
The Okinawa Times reported Saturday that at least 261 flights serving Naha International Airport were canceled, affecting more than 31,500 passengers. It also suspended all commuter trains in the Kyoto, Osaka and Kobe areas by noon, according to its website.
Packing maximum gusts of 216 kilometres (134 miles) per hour near its centre, Trami was forecast to hit the mainland later Sunday and travel over most of the archipelago, causing extreme weather into Monday, forecasters said.
Trami is then predicted to move across the islands of Kyushu and the main island of Honshu on Sunday, a path similar to that taken by Typhoon Jebi early in September.
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Railway companies and airlines canceled services in central, eastern and western Japan.
Local officials and police said two people had been killed in the storm. I stepped outside the city hall in the afternoon, and the rain was swirling in the very strong wind.
Bullet trains and other train lines were shutting down while the storm passed.
Osaka's Kansai International Airport, which was flooded by a typhoon last month, . has shut its runways.
The airport also was closed for this latest typhoon.
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Officials piled up sandbags to avoid a repeat of flooding seen during the previous storm.
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.
Western regions are still recovering from the most powerful typhoon to strike the country in a quarter of a century in early September.
The agency warned of mudslides, torrential rains and powerful winds in northern and north-eastern Japan.
Also in September, a magnitude 6.6 quake rocked the northern island of Hokkaido, sparking landslides and leaving more than 40 people dead.
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