A wave of one metre (three feet) is expected to hit the coast of the Sea of Japan, north of Tokyo, the nation's meteorological agency said.
The quake registered six on the Japanese scale, which goes up to a maximum of seven and was felt in the capital, which is more than 300 kilometres away.
An official of the disaster management office of Niigata prefecture, the epicentre of the quake, told AFP: "We do not have a precise picture of the impact as we are still collecting information. But so far there have been no report of injuries or casualties."
Separately, a fire department official in the region said two elderly women were sent to hospital following falls but "they were conscious."
The earthquake struck at a late hour in mainly sparsely populated areas so it was not easy to evaluate the damage immediately.
Witnesses cited by national broadcaster NHK said they experienced strong shaking that knocked some books off shelves and moved some furniture.
The broadcaster showed images of some cups and glasses smashed on the floor of a restaurant.
The US Geological Survey put the magnitude of the quake at 6.4.
Officials immediately stopped bullet train services in the region as a precautionary measure, according to NHK, which also said thousands of households were left without power.
The meteorological agency said some small waves had already reached some coastlines of Yamagata and Niigata, in the northwest of the country.
The agency warned that it is "dangerous" to stay near the coast or in the sea. "Do not approach or enter the sea until the advisory is lifted," it said.
A minor change in sea levels had already been monitored on a small island off Niigata, it added.- 'No abnormalities' -
"All nuclear power plants have reported no abnormalities," government spokesman Yoshihide Suga told reporters.
"Strong jolts may continue," warned Suga, adding that authorities were checking for signs of damage or injuries.
Some local roads were also closed after the earthquake, which struck at around 10:22pm local time (1322 GMT).
Japan sits on the Pacific "Ring of Fire" where many of the world's earthquakes and volcanic eruptions are recorded.
A powerful quake rocked northern Japan in September and triggered massive landslides that killed 44.
Last June, a deadly tremor rocked the Osaka region, killing five people and injuring over 350.
On March 11, 2011, a devastating 9.0-magnitude quake struck under the Pacific Ocean, and the resulting tsunami caused widespread damage and claimed thousands of lives.
Niigata itself has a history of large earthquakes.
In 2004 a 6.8-magnitude quake hit, killing 68 people, including elderly who died in the days and weeks after the first tremor from stress and fatigue.
The area was also hit by a magnitude-6.8 quake in 2007, leaving 15 people dead.