NHK footage also showed a huge landslide in Atsuma in Hokkaido, the Japan Times reports.
The International Tsunami Information Centre said there was no tsunami threat.
A Kiwi staying near the epicentre at Obihiro has described the moment the quake hit.
Mark Bryan said he woke at 3.08am local time to an early warning alarm in his hotel.
"Fairly impressive shaking on 9th floor. Evacuated into the streets but all good. Now on bus to airport but significant delays with no power and some roads damaged."
The quake follows Typhoon Jebi which swept ashore causing widespread flooding and deaths.
The quake's epicenter is about 27.3km east of the city of Tomakomai, which has a population of about 175,000, and 64.8km southeast of Sapporo, which is a major metropolitan area of 1.9 million people.
The Kyodo news service reports that in Tokyo, the central government set up a liaison unit at the crisis management centre of the prime minister's office to gather information on the temblor.
Chief Cabinet Secretary Yoshihide Suga says Prime Minister Shinzo Abe instructed officials to ascertain the extent of damage and extend a helping hand to those affected.
additional reporting AP
