The discovery of the three victims -- two women and one man -- raised the death toll from Saturday's quake in the north of the country to nine, with more than 220 others injured.

Military helicopters roared across the rice fields and rolling hills of the region, plucking to safety hundreds of people who were cut off from the world as the tremor snapped bridges and buried roads with landslides.

At the Komanoyu hotel, a secluded inn with natural hot springs that had survived for nearly four centuries, soldiers pulled the bodies of the three victims from a massive heap of mud, wood and shattered furniture.

"It's more difficult than expected to deal with this mud," said Masahiro Ishiba, a soldier heading a team of 300 soldiers and civilians who cut through the debris and tried to dig a ditch to drain water that had collected.

"Right now we're finding it tough to make much progress. But all of us are doing all we can," he told public broadcaster NHK.

A total of 11 people remain unaccounted for, including four at the hotel.

But the mud outside the hotel was swelling up, said Norio Sato, a senior local official in the hard-hit town of Kurihara, adding that landslide risks in seven other places had also hampered recovery efforts.

The earthquake measured 7.2 on the Richter scale, making it the strongest in inland Japan in eight years.

Dozens of frightened people were set to spend a second night in shelters after the earthquake, which was followed by more than 270 aftershocks.

Tatsuo Oikawa, 80, had an emotional reunion with his daughter who searched for him throughout the night before finding that he, like dozens of others, had stayed in a makeshift shelter out of fright.

"It's so wonderful that you survived," said his 47-year-old daughter, Sayako, her eyes turning red with tears.

Japan endures about 20 percent of the world's powerful earthquakes and has built an infrastructure intended to withstand the impact of tremors.

Emperor Akihito, visiting nearby Akita prefecture on a previously scheduled event, said that he shared the "sorrow and pain" of the earthquake victims.

"I hope peace will return to people's daily lives as soon as possible," the emperor said.

Hidetsugu Takahashi, 60, was taking pictures of the scenery of this region 350 kilometres (220 miles) north of Tokyo when the quake struck.

He was airlifted to the main town of Kurihara from a country inn, where he said most guests spent the night in the candlelit lobby because the furniture was damaged in their rooms.

"I saw big rocks fall down that were as big as eight metres (yards) wide. It was so scary," Takahashi said.

"I stayed inside my car at night because I was afraid of aftershocks. I couldn't sleep," he said.

At the heliport in Kurihara, two ambulances were on standby to take any injured to hospital, but most evacuees were content just having tea and snacks.

Kirino Miura, 75, was airlifted along with her husband as the water level rose in a river next to their house.

"I saw rocks falling down from the cliffs. It's frightening. We didn't have any choice but to evacuate," she said.

But around 30 people were resisting calls by authorities to leave, saying they had to take care of their farmland, said military spokesman Lieutenant Shoichi Chiba.

"The administration is trying to persuade them to evacuate. It's not as if we won't take care of their land," Chiba said.

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