Thousands of people took shelter in crowded evacuation centres Tuesday as forecasters warned heavy rain could trigger mudslides in Japan's northwestern coast.

Nearly 13,000 people packed into schools and other secure buildings in the quake zone 260 kilometres northwest of Tokyo, the Fire and Disaster Management Agency said.

A man makes his way through a split road after a strong earthquake rocked Niigata prefecture in northwestern Japan on Monday.
(Mainichi Shimbun/Associated Press)

A second strong earthquake shook Japan on Monday just hours after the earlier tremor killed at least nine people, injured hundreds of others and sparked a fire and leak at a large nuclear power plant.

The 6.6 magnitude quake occurred at 11:18 p.m. local time in the Sea of Japan off the country's west coast near the Kyoto region, Japan's meteorological agency reported.

No tsunami alerts were issued in the latest tremor. Reuters news agency reported witnesses seeing buildings in Tokyo swaying during the quake.

Earlier Tuesday, at around 10:13 a.m., a 6.8 magnitude quake struck off the coast of the Niigata area, about 260 kilometres northwest of Tokyo.

That quake destroyed dozens of houses in the hardest-hit city of Kashiwazaki.

Japan's weather agency issued heavy rain, flooding and lightning warnings Tuesday for the area, which had been buffeted by strong rains in the days before the quake, softening the ground and increasing the likelihood of landslides, officials said. Up to six centimetres of rain is expected by Wednesday morning in Kashiwazaki, the local observatory said.

"The damage is more than we had imagined," Kashiwazaki Mayor Hiroshi Aida said while inspecting damaged areas, adding the water supply had been disrupted.

"We want to restore the water as soon as possible so more people can return home," he said.

The first earthquake also caused a fire at the nuclear plant's electrical transformer. 

The plant automatically shut down and the fire was put out shortly after noon, said Motoyasu Tamaki, a Tokyo Electric Power Co. official.

About 315 litres of water leaked out of the building housing one of the reactors, said Katsuya Uchino, another Tokyo Electric official.

Black smoke rises from a burning electrical transformer near one of the Kashiwazaki nuclear plant's four reactors following the earthquake.
(Kyodo News/Associated Press)

Uchino said the water contained a tiny amount of radioactive material — a billionth of the guideline under Japanese law — and is believed to have flushed into the Sea of Japan.

A company statement said the leak had stopped and that there had been no "significant change" in the seawater under surveillance, and no effect on the environment.

Four women and three men, all elderly, were crushed to death when buildings collapsed in the first tremor, police and NHK, Japan's public broadcaster, said. More than 900 people suffered injuries including broken bones, cuts and bruises.

Area hospitals were having trouble treating the injured because of damages to the facilities, the CBC's John Northcott reported from Tokyo.

Nearly 300 homes in the city were destroyed and about 10,000 people fled to evacuation centres, officials said. The force of the quake buckled seaside roads and bridges, and one-metre-wide fissures could be seen in the ground along the coastline.

"I was so scared — the violent shaking went on for 20 seconds," local resident Ritei Wakatsuki told the Associated Press by telephone from Kashiwazaki. "I almost fainted by the fear of shaking."

The meteorological agency also issued tsunami warnings for the coastal area of Niigata, but the warnings were later lifted.

Aftershocks possible for a week: official

In between the two strong quakes, the Niigata area was plagued by a series of aftershocks, the strongest of which was magnitude 5.8. Meteorological agency spokesman Koichi Uhira warned that the aftershocks could continue for a week.

Prime Minister Shinzo Abe said he would head to the damaged area.

"We want to do all we can to ensure safety … and to quell everyone's concerns," the prime minister said after interrupting a campaign stop in the north for upcoming parliamentary elections. "I want to get a picture of what happened and also want everyone to feel a little bit more secure."

Japan sits atop four tectonic plates and is one of the world's most earthquake-prone countries. The last major quake to hit Tokyo killed about 142,000 people in 1923, and experts say the capital has a 90 per cent chance of suffering a major quake in the next 50 years.

In October 2004, a magnitude-6.8 earthquake hit Niigata, killing 40 people and damaging more than 6,000 homes. It was the deadliest to hit Japan since 1995, when a magnitude-7.2 quake killed 6,433 people in the western city of Kobe.

With files from the Associated Press