The toll had already reached the total of last winter, which was the highest in two decades, reported semi-public broadcaster NHK, adding that, based on its tally, 88 people had been killed.
A 54-year-old man died in hospital after being rescued from the wreckage of his garage, which had been crushed by the accumulated snow, local media reported.
The man was trapped for two hours under the wreckage in Myoko city, northwest of Tokyo, one of the areas hardest hit by heavy snowfalls in the past month, the reports said.
Two mentally disabled men were buried under a wooden-framed house that was also crushed under snow in nearby Joetsu, the reports said. One managed to escape but the other died.
Temperatures rose Saturday in many areas heavily blanketed by snow, causing avalanches, including one that was about 300 to 400 meters long (990 to 1,320 feet) and 30 to 40 meters wide at a ski slope.
Police were investigating whether anyone was injured on the slope in Shimane prefecture, west of Tokyo.
The Japanese Meteorological Agency issued warnings for avalanches caused by a rapid rise in temperatures and increase in rain over the weekend in areas covered by heavy snow.