As much as 27 centimetres (10.6 inches) of snow was recorded in Tokyo by late Saturday, the heaviest fall in the capital for 45 years, according to the meteorological agency.
The snow storm hit the capital on the eve of its gubernatorial election. Observers say the heavy snowfall may affect voter turnout in the city of 13 million people.
As a depression moved along the Pacific coast north Saturday, the northeastern city of Sendai saw 35 centimetres (13.8 inches) of snow, the heaviest in 78 years.
Local media said at least five people have been killed in snow-linked accidents -- mostly crashes after their cars skidded on icy roads.
Public broadcaster NHK reported more than 600 people were injured across the nation.
More than 20,000 households were still without electricity early Sunday while airlines cancelled 200 domestic flights a day after more than 740 flights were grounded Saturday.
Nearly 5,000 people were stranded at Narita airport Saturday as traffic linking the airport to the capital was disrupted, NHK said.
Further snowfall is expected Sunday in northern Japan, the weather agency said.