The typhoon, rated by Tropical Storm Risk as a category 1, the lowest on a five-point scale, killed two people and injured nearly 130, public broadcaster NHK said.
Kansai International Airport in Osaka, which was temporarily crippled by a typhoon earlier in the month, was closed and plans to reopen on Monday, the airport said.
According to local media, the woman in her 60s was swept away by gusts in a gutter while working with her husband in their ricefield.
A powerful typhoon is battering Japan, causing widespread travel disruption.
Footage showed winds and rain from the typhoon, rated category 1 by Tropical Storm Risk, with category 5 the highest, sweeping through towns and uprooting trees.
Japan issued evacuation orders and warnings to about 700,000 households in southern and western Japan.
As the typhoon barrelled east, rail authorities took the highly unusual step of cancelling evening train services in Tokyo, one of the world's busiest networks, urging passengers to shelter indoors when the storm hits.
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More than 185,000 homes and offices had power outages as of 9 p.m. on Sunday in the southern Kyushu region, according to Kyushu Electric Power Co., while about 118,000 buildings were without power in Okinawa as of 9:50 p.m. according to Okinawa Electric Power Co.
On Sept. 4, Typhoon Jebi also flooded a terminal and a runway at Kansai International Airport, built on an artificial island, and caused a tanker to smash into and damage a bridge connecting the airport with the mainland, stranding thousands of people at the airport at one point.
East Japan Railway stopped all train services in and around Tokyo at 8:00 pm, shortly before the typhoon hit the Japanese capital.
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.
And last month, a magnitude-6.6 natural disaster rocked the northern island of Hokkaido, sparking landslides and killing more than 40 people.
The Japan Meteorological Agency said on Sunday morning Trami was a very strong category storm, with national broadcaster NHK reporting that it could be the strongest typhoon to make landfall in Japan in 25 years.
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