The quake with a preliminary magnitude of 7.6 triggered waves of about one metre along parts of the Sea of Japan coast on Monday, with a larger wave expected, public broadcaster NHK reported.
The Japan Meteorological Agency has issued tsunami warnings for the coastal prefectures of Ishikawa, Niigata and Toyama, marking the first major warnings since the March 2011 earthquake and tsunami that struck northeast Japan.
Japan has issued tsunami alerts and told people to evacuate seaside areas after a strong earthquake. (AP PHOTO)
A major tsunami warning means there is a possibility of waves of more than 3m.
Russia also issued tsunami warnings in its far eastern cities of Vladivostok and Nakhodka.
Some houses have been destroyed and army units have been dispatched to help with rescue operations, top government spokesperson Hayashi Yoshimasa told reporters, adding that authorities were still assessing the extent of the damage.
More strong quakes in the area, where seismic activity has been simmering for more than three years, could occur in the coming days, JMA official Toshihiro Shimoyama said.
In comments to the press shortly after the quake struck, Prime Minister Fumio Kishida also warned residents to prepare for more disasters.
The Japan Meteorological Agency has issued tsunami warnings for several coastal prefectures. (AP PHOTO)
"Residents need to stay on alert for further possible quakes and I urge people in areas where tsunamis are expected to evacuate as soon as possible," Kishida said.
"Run!" flashed a bright yellow warning aired on NHK advising residents in specific areas of the coast to immediately evacuate their homes.
Footage by the broadcaster showed a building collapsing in a plume of dust in the coastal city of Suzu and residents in Kanazawa city cowering under tables as tremors shook their homes.Â
The quake jolted buildings in the capital Tokyo on the opposite coast.
More than 36,000 households had lost power in Ishikawa and Toyama prefectures, utilities provider Hokuriku Electric Power said.
High-speed rail services to Ishikawa have been suspended while telecom operators Softbank and KDDI reported phone and internet service disruptions in Ishikawa and Niigata, according to their websites.
Japanese airline ANA turned back four planes midair as they headed to airports in Toyama and Ishikawa, while Japan Airlines cancelled most of the flight services to Niigata and Ishikawa regions for the rest of the day, according to TV Asahi.
A temple in Ishikawa popular with New Year tourists was damaged in the earthquake. (AP PHOTO)
Japan's Nuclear Regulation Authority said no irregularities have been confirmed at nuclear power plants along the Sea of Japan, including five active reactors at Kansai Electric Power's Ohi and Takahama plants in Fukui Prefecture.
Hokuriku's Shika plant in Ishikawa, the closest nuclear power station to the quake's epicentre, had already halted its two reactors before the quake for regular inspections and was not impacted by the quake, the agency said.
The 2011 earthquake and tsunami killed almost 20,000 people and devastated towns and nuclear meltdowns in Fukushima.
Monday's quake struck during the January 1 public holiday when millions of Japanese traditionally visit temples to mark the new year.
In Kanazawa, a popular tourist destination in Ishikawa, images showed the remnants of a collapsed torii gate strewn at the entrance of a shrine as anxious worshippers looked on.
