Transport authorities launched an investigation Sunday into the incident, which occurred Saturday in Akita, Kyodo News reported.
About 130 passengers were on board, officials said.
The first of the train's six cars jumped from the rails at about 4:05 p.m. Saturday, Kyodo News reported.
The train had been running at a reduced speed of 12 mph due to the severe snowfall in the area, Accuweather.com said.
The current snow depth in the area ranges from 18 inches to 90 inches, Accuweather.com said, and winds were averaging 25 to 35 mph for much of the day.
Bullet train services have been suspended due to the snow, Accuweather.com said.