Two elderly women were killed on the northernmost island of Hokkaido, Kyodo News reported, with one hit by a snow-plough and another buried when a warehouse collapsed under the weight of fallen snow.
Two men, meanwhile, died in traffic accidents on snow-bound roads, one in Hokkaido and the other in Hiroshima further south, police said.
Another man, 68, was discovered dead outside his home in Niigata on the main island of Honshu, police said, with reports saying he had fallen from the garage roof while removing snow.
Reports said the bullet train network was also struggling to stick to its timetables.
The mountain town of Tsunan in Niigata prefecture, near the Sea of Japan (East Sea) coast, was smothered in 204 centimetres of snow, with parts of Hokkaido getting as much as 70 centimetres in 24 hours, the Japan Meteorological Agency (JMA) said.
The snow is accompanied by strong gusting winds of up to 140 kilometres (87 miles) an hour, which is causing tidal surges and sparking warnings to stay away from the water's edge.
Parts of northern Honshu could expect up to 80 centimetres of snow by breakfast time on Friday, the JMA said.
