Sunday's earthquake, which struck off the north coast of Ishikawa, toppled buildings and triggered landslides, as well as disrupting power, water mains and communications lines.
A 52-year-old woman was crushed to death by a falling stone lantern and at least 193 others were injured mostly when they fell or were hit by falling objects and broken glass, local officials said.
Shinzo Abe, Japan's prime minister, told a parliamentary committee on Monday the earthquake had knocked down at least 68 homes and partially destroyed another 164.
Most of the injuries and damage was in Wajima city, about 310 kilometers northwest of Tokyo.
"The government will make every effort to help the victims of the earthquake so they can resume normal lives," Abe said.
Japanese media reported that thousands of homes were still without water supply but electrical power has almost been restored to all areas.
Most train and air transport services had resumed operations.
The last major earthquake to cause casualties in the area, not considered a quake-prone region, was in 1933, when three people died.
In October 2004, a magnitude-6.8 earthquake hit northern Japan, killing 40 people and damaging more than 6,000 homes.
It was the deadliest to hit Japan since 1995, when a magnitude-7.2 quake killed 6,433 people in the western city of Kobe.