Residents rushed to evacuate from coastal areas as the quake, according to public broadcaster NHK, triggered waves of more than three feet along parts of the Sea of Japan.
It also destroyed buildings, knocked out power to thousands of homes and disrupted flights in the region.
Following the quake, which had a preliminary magnitude of 7.6, the Japan Meteorological Agency has issued tsunami warnings for the coastal prefectures of Ishikawa, Niigata and Toyama.
The major tsunami warning was the first since 2011.
Russia also issued tsunami warnings in its far eastern cities of Vladivostok and Nakhodka.
Tourist Baldwin Chia experienced the quake from Japan's alps.
"So the whole room was shaking, the TV was shaking. I had to keep everything on the table. Yeah, I do, I did feel safe in my room, though. But everything else was shaking."
Japan's prime minister Fumio Kishida said on NHK that authorities are assessing the extent of any damage and residents need to prepare for more potential tremors.
A Japanese utilities provider said more than 36,000 households had lost power in Ishikawa and Toyama prefectures.
