At least two people were killed and 45 injured by a magnitude-6.5 earthquake that knocked down houses and buckled roads in southern Japan.

Both victims are from the hardest-hit town of Mashiki, about nine miles east of Kumamoto city on the island of Kyushu, said Kumamoto prefecture disaster management official Takayuki Matsushita.

Earlier, Japanese Red Cross Kumamoto Hospital said it had admitted or treated 45 people, including five with serious injuries.

The quake struck at 9.26pm on Thursday at a depth of seven miles near Kumamoto city on the island of Kyushu, the Japan Meteorological Agency said. There was no tsunami risk.

"The shaking was so violent I couldn't stand still," said Hironobu Kosaki, a Kumamoto prefectural police night-duty official.

Japan's chief cabinet secretary Yoshihide Suga said at least 19 houses collapsed, and hundreds of calls came in reporting building damage and people buried under debris or trapped inside.

"Because of the night darkness, the extent of damage is still unclear," he said.

The damage and calls for help are concentrated in the town of Mashiki, about 800 miles south-west of Tokyo, Japan's Fire and Disaster Management Agency said

One of the victims in Mashiki died after being pulled from some rubble, and the other was killed in a fire, Matsushita said. A third person rescued from under a collapsed building is in a state of heart and lung failure.

Matsushita said rescue operations were repeatedly disrupted by aftershocks.

"There was a ka-boom and the whole house shook violently sideways," Takahiko Morita, a Mashiki resident said in a telephone interview with Japanese broadcaster NHK. "Furniture and bookshelves fell down, and books were all over the floor."

Morita said some houses and walls collapsed in his neighbourhood, and the water supply had been cut off.

Dozens of people evacuated their homes and gathered outside Mashiki town hall. Some wrapped blankets around their shoulders against the springtime chill.

Prime minister Shinzo Abe told reporters that the government has mobilised police, firefighters and self-defence troops for the rescue operation.

"We'll carry out relief operation through the night," he said.

Suga said there are no abnormalities at nearby nuclear facilities. The epicentre was 74 miles north-east of Kyushu Electric Power's Sendai nuclear plant, the only one operating in the country.

Most of Japan's nuclear reactors remain offline following the meltdowns at Tokyo Electric Power's Fukushima plant in 2011 after a magnitude 9.0 earthquake triggered a huge tsunami.

There were multiple aftershocks, the largest one with a preliminary magnitude of 6.4 shortly after midnight, according to the Japan Meteorological Agency.

The US Geological Survey measured the initial quake's preliminary magnitude at 6.2. It upgraded its damage assessment to red, meaning extensive damage is probable and the disaster likely widespread.