At least 9 people were killed in Thursday's earthquake, Chief Cabinet Secretary Yoshihide Suga said Friday.
The government had previously said 16 people died, but Suga told reporters later that this figure was incorrect and officials had mistakenly also counted those who suffered heart attacks due to the quake.
Search and rescue teams are still looking for 26 people missing in the western town of Atsuma in Hokkaido Prefecture. Prime Minister Shinzo Abe said that more than 22,000 people were involved in the rescue efforts, as the northern island still deals with the after effects of the magnitude-6.6 quake, which caused landslides that buried homes and other buildings.
Electricity was restored to around 1.4 million buildings as of Friday morning, Abe added, around half of all of those which initially lost power.
More than 150 people were injured by the quake, mostly in Sapporo, said Kazuya Isaki, an official with the Crisis Management Office of Hokkaido Prefecture Government. Dozens of people were reported missing in Atsuma, near the epicenter of the quake, where four of the deaths occurred.
Public broadcaster NHK reported that flights and public transport across the region had been brought to a standstill.
Nearly 3 million households lost power, according to the Hokkaido Electric Power Company. Officials said a main power station lost operations, affecting other sites. Independently owned power generators were assisting.
"The electric supply was stopped to Tomari nuclear plant, but it can operate without external electric supply for one week," Chief Cabinet Secretary Yoshihide Suga said.
The powerful quake lasted almost a minute, jolting residents from their beds and collapsing roads.
Near the epicenter, landslides wiped out houses in the tiny town of Atsuma, home to 40 residents. Officials said multiple people were still missing hours after the initial quake.
Photos from Sapporo, Hokkaido's main city on the western part of the island, showed huge cracks in the street and subsided houses.
More than 4,000 defense force soldiers have been deployed to help with rescue operations, Prime Minister Shinzo Abe said, and that number could rise to 25,000 if needed.
Helicopter rescue crews were also dispatched and have airlifted around a dozen people to safety. Evacuation shelters have been set up in many towns and cities around the region.
Aftershocks were continuing Thursday morning, and could pose a risk for the next week, according to the Japan Meteorological Agency, which warned residents of the increased risk that buildings could collapse near the epicenter of the original quake.
Thursday's earthquake comes as much of Japan is still dealing with the effects of Typhoon Jebi, the strongest such storm to hit the Japanese mainland in 25 years.
High winds smashed a tanker into a bridge, forced one of the country's largest airports to close and left at least 10 people dead.
On Japan's main island of Honshu, nine cities and towns issued compulsory evacuation orders. A further 53 issued non-compulsory evacuation orders.
Before it made landfall, the storm had sustained winds of 140 kilometers per hour (87 mph) and gusts of 165 kmh (102 mph), the equivalent of a Category 1 Atlantic hurricane.