Earlier, the weather agency issued tsunami warnings for a broad swath of the country's western coast, including Ishikawa, Fukui, Niigata, Toyama, Yamagata, and other prefectures, following the earthquakes.
Strong quakes, with major ones measured at up to 7.6 magnitude, struck a wide area on the Sea of Japan coast in central Japan earlier in the day, the JMA said.
A tsunami with about 3-metre-high waves was expected to hit Niigata and other prefectures on the western coast of Japan. Smaller tsunami waves were already confirmed to have reached the coastline, according to NHK.
The weather agency said the latest major temblor occurred at 4:10 p.m. local time (0710 GMT) at a shallow depth, registering a maximum of 7 on the Japanese seismic intensity scale on the Noto Peninsula in Ishikawa Prefecture.
It also shook buildings in central Tokyo.
The temblor's epicentre was located in Ishikawa's Noto region, at Wajima, 30 km east-northeast, at 37.5 degrees north latitude and 137.2 degrees east longitude. (UNI)