"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 Saturday morning's 7.0-magnitude 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 occurred very close to the surface and caused violent shaking.
  
The eruption of a nearby volcano fuelled fears, although seismologists saw no 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 Saturday'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 fatalities occurred when a fire ripped through an apartment complex in the town of Yatsushiro, a local official said.
  
In nearby Kumamoto city, an AFP journalist said he was jolted awake by powerful shaking, which sent the television set in his hotel room crashing to the floor. Staff urged guests to evacuate.
  
Kumamoto airport was forced to close after a ceiling collapsed, Jiji Press reported, with no immediate plans to resume flights. Communications in the area were spotty.
  
By nightfall more than 100,000 households were still without electricity.

Japan's Kyodo news agency reported that about 380,000 homes in Kumamoto were cut off from water supplies.
 
Japan's Meteorological Agency said rain was expected to hit Kumamoto overnight and some areas would see heavy downpours on Sunday, raising the risk of further landslides in places where soil and rock has already been loosened.
  
Twitter user @kbbblove pleaded for help for "about 30 people" still trapped at a campsite.
  
"Please go rescue them before the rain and wind comes because it's close to a mountain," the user wrote.
  
The town of Misato urged more than 10,000 people to evacuate Saturday for fear of a landslide, national broadcaster NHK reported.
  
The government is to send 25,000 troops and more than 1,000 emergency responders including firefighters and police to the stricken region.
  
"It has already started raining and the rain and winds are expected to get stronger," Prime Minister Shinzo Abe said at an emergency meeting in the evening.
  
"Night-time rescue missions will be very difficult but people are waiting,"
he said.
  
The government is also preparing to provide enough food for all the evacuees for three days.
  
Japan, one of the world's most seismically active countries, suffered a massive undersea quake on March 11, 2011 that sent a tsunami barreling into its northeast coast.
  
Some 18,500 people were left dead or missing, and several nuclear reactors went into meltdown at the Fukushima plant in the worst atomic accident in a generation.
  
Japan's only working nuclear plant, southwest of Saturday's epicenter, was unaffected by the quakes, the government has said. (AFP)