Japan's meteorological society reevaluated the quake, stating it was actually 6.8 magnitude-strong, while its epicenter was located at a depth of some 10km. However, it's said that shallow tremors can cause more damage to the Earth's surface.
Authorities lifted a 0.2-1.0 meter tsunami warning for the region after waves several centimeters high struck parts of the Niigata coast.
The magnitude 6.4 quake, according to the U.S. Geological Survey (USGS), lasted for as long as 20 seconds and damage included a landslide that struck a road, according to public broadcaster NHK.
All seven reactors at the Kashiwazaki-Kariwa nuclear plant in Niigata were off line and no abnormalities have been reported.
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The quake struck at 10.22pm local time (2.22pm BST) at a depth of about 10km about 53 miles northeast of the island of Honshu.
Japan sits on the Pacific "Ring of Fire" where numerous world's earthquakes and volcanic eruptions are recorded.
"The seafloor expression of the boundary between the Pacific and North America plates lies 300 km off the east coasts of Hokkaido and Honshu at the Kuril-Kamchatka and Japan trenches".
"The 1958 M 8.4 Etorofu, 1963 M 8.6 Kuril, 2003 M 8.3 Tokachi-Oki, and the 2011 M 9.0 Tohoku earthquakes all exemplify such megathrust seismicity".
The agency warned that it is "dangerous" to stay near the coast or in the sea.