Most services have been restored, though disruption to train services is still reported and some smaller roads remain blocked by landslides.
Military helicopters are scouring the region for trapped quake victims, but no deaths have yet been reported.
Experts said the depth of the quake had prevented more serious casualties.
"Despite such a powerful earthquake, the damage was minimum because the epicentre was so deep," Ryohei Morimoto, geologist and emeritus professor of geology at Tokyo University, told AP news agency.
"It was really lucky."
The earthquake is the latest in a series of tremors to hit the north of the main Japanese island of Honshu. Its epicentre was more than 100km (62 miles) underground.
The earthquake struck just after midnight on Thursday (Wednesday 1500 GMT) in Iwate prefecture, shattering windows and triggering landslides.
It was felt more than 450km to the south-west, in the capital, Tokyo - startling Prime Minister Yasuo Fukuda in his bedroom.
At least 109 people were injured, 16 seriously, according to the National Police Agency. Several people suffered broken bones as they were thrown to the floor.
Pictures showed large boulders strewn across a highway.
Military aircraft have been ordered to check the region for possible trapped survivors, but were being hampered by fog and light rain.
"There were no reports of deaths or people buried alive," said government spokesman Nobutaka Machimura.
The quake pushed over tombstones at a temple in Hachinohe
"But the prime minister has ordered us to continue checking."
At a temple in the city of Hachinohe, the quake toppled gravestones, breaking some and prompting residents to rush to try to repair the damage.
No damage was reported to any nearby nuclear power stations.
Japan is one of the world's most earthquake-prone countries and experiences thousands of tremors each year.
Just over a month ago, a 7.2-magnitude quake struck in the same region, leaving 23 people dead or missing.