Japan's Meteorological Agency said there was no danger of a tsunami from the temblor, which had a preliminary magnitude of 6.8. It struck shortly after midnight about 65 miles underground and centered just off the coast of Iwate, 280 miles northeast of Tokyo.
At least 109 people were injured, including 16 seriously, according to the National Police Agency. Japan's Kyodo News agency said 131 people were injured, citing its own tally.
The earthquake caused strong shaking of up to 40 seconds in large parts of northern Japan, official said.
"Everything has fallen off the shelves, scattered all over the floor," grocery store owner Tomio Kudo told national broadcaster NHK from the town of Hirono, where the shaking was most violent. "Even a big refrigerator has moved about 30 centimeters (1 foot)."
Several nuclear power plants in the region continued operations after inspection by plant workers found no problems, the Ministry of Economy, Trade and Industry said in a statement.
The quake caused a blackout at more than 8,000 homes, it said.
Japan's "bullet" super-express trains were suspended in some areas, according to operator East Japan Railway Co.The earthquake also triggered landslides at several locations, the police agency official said. Details were not immediately available.
Relief workers and local officials hit the streets to take a closer look to the affected areas in daylight Thursday. A team of government officials headed by Disaster Minister Shinya Izumi also arrived in Iwate.
"We must grasp the extent of damage as quickly as possible so that we can immediately take necessary steps," Prime Minister Yasuo Fukuda told reporters.
Police said some of the more serious injuries included a woman in Hirono who broke a leg falling down stairs and another woman in Aomori city who broke her hip fleeing out a window.