Snow is falling heavily on the coast, along the Sea of Japan. Storms have also plastered parts of Shikoku and Kyushu in the southwest, where snow is rarely seen.
Transportation systems in the areas have been badly affected. Several residents have been injured on slippery roads.
In Ozu City, Ehime Prefecture, a train collided with a tree that had toppled under the weight of accumulated snow. No one was injured.
One passenger said, "I felt an impact, as if the train had mounted something. It turned out that the train was dragging a tree that had fallen."
In Tokushima Prefecture, the rare snowfall triggered a series of accidents that led to heavy congestion on a national roadway.
Local authorities say 9 people were injured in traffic accidents on frozen roads.
In the city of Amakusa in Kumamoto Prefecture, a large truck and other vehicles became stranded on a road.
At an airport in the city, flights had to be cancelled.
Weather officials expect the snow storms to continue over the next 2 days, mainly along the Sea of Japan coast.
They are advising residents to be careful on icy roads and to be on guard against possible avalanches.