Hundreds of people have been evacuated from their homes and hundreds more injured, as more than 3 ft of snow fell in some areas.
The snow forced airports to cancel flights and closed roads as it barreled past Tokyo on Saturday.
Forecasters are warning of blizzards and avalanches later, as the storm moves north towards Hokkaido.
Kyodo news agency reported deaths in several prefectures near Tokyo, and other deaths as far south as Oita on Kyushu island.
Reports said roofs of buildings had collapsed under the weight of snow in some areas, and hundreds of drivers had been left stranded in miles-long traffic jams.
Some 11in of snow was dumped on Tokyo on Friday and Saturday, and several other cities reported record snowfall.
It is the second major snowstorm to batter Japan in a week.
Last week Tokyo residents were warned of a severe snowstorm for the first time in more than a decade.
Eleven people were also killed in that storm, with more than 1,000 injured nationwide.
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