The quake with a preliminary magnitude of 7.6 struck in the middle of the afternoon on Monday, destroying buildings, knocking out power to tens of thousands of homes and prompting residents in some coastal areas to flee to higher ground.
It also triggered waves about 1 meter (3.3 ft) high along Japan's long western seaboard as well as in neighbouring South Korea.
Army personnel were dispatched to help with rescue operations, while one local airport was shut down after the quake tore open cracks in the runway.
An elderly man was pronounced dead after a building collapse in Shika Town in Ishikawa prefecture, broadcaster NTV reported citing local police.
Kyodo News reported four deaths in Ishikawa, citing the Prefectural Crisis Management Team, including a man and woman in their 50s, a young boy, and a man in his 70s. The Asahi newspaper cited police as saying a man in his 90s had been pulled from the wreckage of a building and taken to hospital but confirmed dead.
Japanese Prime Minister Fumio Kishida told reporters late on Monday that it was proving difficult for search and rescue teams to reach the worst affected areas due to blocked roads.
President Joe Biden said in a statement that the United States was ready to provide any necessary help to Japan after the earthquake.
"As close allies, the United States and Japan share a deep bond of friendship that unites our people. Our thoughts are with the Japanese people during this difficult time," he said.
The Japanese government said that as of Monday night it had ordered more than 97,000 people in nine prefectures on the western coast of main island Honshu to evacuate. They were spending the night in sports halls and school gymnasiums, commonly used as evacuation centers in emergencies.
Almost 33,000 households remained without power in Ishikawa prefecture early on Tuesday morning, according to Hokuriku Electric Power's website.
The Imperial Household Agency said that following the disaster it would cancel Emperor Naruhito and Empress Masako's slated New Year appearance on Tuesday.
Nuclear Plants
The quake comes at a sensitive time for Japan's nuclear industry, which has faced fierce opposition from some locals since the 2011 earthquake and tsunami that triggered nuclear meltdowns in Fukushima. Whole towns were devastated in that disaster.
The Nuclear Regulation Authority said no irregularities were found at nuclear plants along the Sea of Japan, including five active reactors at Kansai Electric Power's Ohi and Takahama plants in Fukui Prefecture.
Hokuriku Electric's Shika plant, the closest to the epicenter, had already halted its two reactors before the quake for regular inspections and saw no impact from the quake, the agency said.
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