Shallow quakes tend to inflict more damage on the Earth's surface.
The quake struck at 10.22pm local time on Tuesday at a depth of 12km, the USGS said.
Predictions by the agency indicate that the tsunami could be as high as a yard along the coast of the northwestern prefectures of Yamagata, Niigata and Ishikawa. Its impact also raised huge waves up to 40 meters (approximately 131 feet) high that, as people were still reeling from the aftershocks, began crashing into the coast.
Chief Cabinet Secretary Yoshihide Suga said authorities were on standby.
Prime Minister Shinzo Abe told reporters his government would be "on the maximum alert" to prepare for possible rescue operations in the region. Many others, including children, were still awake and sitting against the walls.
A auto in Tsuruoka, Yamagata Prefecture, after Japan was struck by an natural disaster.
The bullet train services in the region were suspended immediately after the jolt. About 9,000 households in Yamagata and Niigata lost power, according to Tohoku Electric Power Co.
And all seven reactors at the Kashiwazaki-Kariwa nuclear plant in Niigata were reported off line and there were no abnormalities.
It added that nuclear power plants close to the epicentre of the quake remained unaffected.
"We put people's lives before anything else", Prime Minister Shinzo Abe said.
NHK showed broken glasses and dishes scattered on the floor of a bar in Tsuruoka which was empty after customers rushed out, leaving behind their half-eaten food on the counter.
Japan sits on the Pacific "Ring of Fire", where numerous world's earthquakes and volcanic eruptions are recorded.
On March 11, 2011, a magnitude 9.0 natural disaster struck under the Pacific Ocean resulting in a tsunami that caused widespread damage and claimed thousands of lives.