More than 90,000 people from the affected area have been evacuated.
Scores of people were feared buried alive on Saturday after two powerful quakes hit southern Japan a day apart, killing at least 41 people, as a forecast storm threatened more devastating landslides.
Homes, roads and railway lines were swept away when huge hillsides collapsed as thousands of tonnes of mud was dislodged by the thunderous seismic tremors. Buildings were reduced to rubble, including a university dormitory and apartment complexes, with dozens of people unaccounted for over a wide area.
"We are aware of multiple locations where people have been buried alive," Chief Cabinet Secretary Yoshihide Suga told a press conference. "Police, firefighters and Self Defense Force (military) personnel are doing all they can to rescue them." More than 90,000 people have been evacuated, including 300 from an area near a dam thought to be at risk of collapse.
A hospital was left teetering by the 7.0 quake, with doctors and patients rushed from the building in darkness. Isolated villages in mountainous areas near the city of Kumamoto were completely cut off by landslides and damage to roads. At least 500 people were believed trapped in one settlement and expected to spend the night in public buildings, reports said.
Aerial footage showed a bridge on a main trunk road had crashed onto the carriageway below it, its pillars felled. The quake came as emergency responders were working to reach areas hit by a 6.2 magnitude tremor that struck late Thursday. Both quakes were very shallow and caused violent shaking.
The eruption of a nearby volcano fuelled fears, although seismologists cautioned there was no evidence of a link to the quake and said activity was limited. Aftershocks continued to rock Kumamoto on Kyushu island and its surroundings, an area unaccustomed to the powerful quakes that regularly rattle other parts of Japan.
Thursday's initial quake affected older buildings and killed nine people, but today's brought newer structures crashing down, including a municipal office in the city of Uto. "The death toll rose to 41," Akira Ito, a spokesman at the Kumamoto prefectural government, told AFP.
Nearly 1,000 people have been hurt, 184 of them seriously, he added. Tokai University announced that two of its students, who were among around a dozen trapped in a dormitory building in Minami-Aso, were now known to have died.
"We offer our sincerest prayers for the two," said a statement on its website. "We're trying to confirm the safety of other students." At least one of the dead was killed when a fire ripped through an apartment complex in the town of Yatsushiro, a local official said.
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 "Cracks caused by an earthquake is seen at a parking lot in Minamiaso town, Kumamoto prefecture, southern Japan")
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