The earthquake 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 (185 miles) away.

The US Geological Survey put the magnitude of the quake at 6.4.

Prime Minister Shinzo Abe told reporters his government would be "on the maximum alert" to prepare for possible rescue operations in the region and warned citizens to be vigilant for strong aftershocks.

At least 16 were injured after the earthquake, local authorities told AFP.

In Niigata, a man in his 30s fell down and broke a bone, a woman in her 60s fell from her wheelchair and sustained light injuries, and two others were also lightly injured, the prefecture's disaster management department said in a statement.

In Yamagata, at least 12 people were injured "but we are still gathering information on details," the prefecture's disaster management official Yusuke Niizeki told AFP.

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.

Officials immediately stopped bullet train services in the region as a precautionary measure, but resumed operation from Wednesday morning, according to NHK.

Thousands of households were left without power temporarily but power supply recovered by Wednesday morning, NHK also said.

An agency official told an emergency news conference that residents in the region should stay vigilant as "a sizeable earthquake may occur again."

The official also warned that bad weather was forecast in the region, which could potentially trigger landslides.

NHK aired footage showing an elementary school ceiling collapsing onto the ground, and small scale landslides in some towns and near railways.

- 'No abnormalities' -

"All nuclear power plants have reported no abnormalities," government spokesman Yoshihide Suga told reporters in a late nationally televised news conference on Tuesday.

"Strong jolts may continue," warned Suga, adding that authorities were checking for signs of damage or injuries.

There were multiple small aftershocks after the main quake.

Some local roads were also closed after the earthquake, which struck at around 10:22 pm (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 more than 350 others.

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, including elderly people 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. (AFP)