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The 6.8 Richter-scale quake struck just after midnight on the mountainous northern tip of Japan's main island of Honshu, shattering windows and triggering landslides that blocked key roads on the Pacific coast.
Some 110 people were injured, according to a tally by public broadcaster NHK. Police said that 15 of them were in serious condition, some having broken bones as the quake threw them to the ground.
Military helicopters scoured the region famed for its blueberry fields and hot-spring resorts to find if anyone was trapped, but low visibility and light rain hampered the operations.
"I've never felt such a big earthquake before in my life," said Kenji Sasaki, a disaster official in the town of Hirono where the walls and ceilings of the municipal head office suffered cracks.
"I was asleep when I felt the jolt but for its entire duration I couldn't move," he said.
Prime Minister Yasuo Fukuda also said he was startled by the quake, which was so powerful that it shook buildings in the capital some 500 kilometres to the south.
"I was just about to fall asleep. I think everyone else was alarmed as well," Fukuda told reporters.
"As a nation we will promptly take appropriate measures," Fukuda said.
"However, it appears that the area is now foggy so it's difficult to assess the situation by helicopters. We would like to clarify the situation as quickly as possible."
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