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Tokyo saw as much as 27cm of snow, on par with last weekend's snowstorms, which were the heaviest in 45 years.
ANA Holdings, Japan's largest carrier, said 338 domestic flights and 12 international flights were cancelled on Saturday due to the heavy snow.
In Kawasaki, west of Tokyo, a train crashed into another after the snow rendered its brakes ineffective, leaving 19 passengers injured. It also snarled traffic on some of Tokyo's most heavily travelled roads.
The heavy snow also caused wide-spread power outages.
Tokyo Electric Power Co Inc, which serves the nation's capital and surrounding regions, said up to 246,000 households were without electricity at one point on Saturday.
As of 12:30pm on Sunday (local time), about 18,000 homes were still without power, the utility said.