The magnitude 6.7 earthquake, which occurred before dawn on Thursday, triggered landslides that buried houses and paralyzed Hokkaido with widespread power and transport cuts.
The death toll had been posted at eight o'clock in the morning, but NHK quoted Abe as reporting on the new total shortly after he held an emergency meeting early Friday.
Another 26 people were missing, disaster management authorities said.
The island, a tourist destination the size of Austria known for its mountains, lakes and seafood, lost all energy after the earthquake when Hokkaido Electric Power Co. closed its fossil fuel-fired power plants as a precautionary measure.
The company had restored power to about 1.31 million of the 2.95 million customers before early Friday, the Ministry of Economy, Trade and Industry said. The Minister of Industry, Hiroshige Seko, could take at least a week to restore power completely.
The earthquake was the second disaster that hit Japan this week after a summer in which the country has been hit by deadly typhoons, floods and an unprecedented heat wave.
Kansai International Airport has been closed since Typhoon Jebi crossed Osaka on Tuesday, although some domestic flights operated by Japan Airlines (JAL) and ANA's low-cost airline Peach Aviation resumed on Friday, carriers said.
At the main airport of Hokkaido, New Chitose, JAL was preparing to restart some flights from around 11:00 a.m. (0200 GMT) Friday, said a spokesman. ANA canceled all flights in the morning but resumed operations normally in the afternoon, a spokesperson said.
JR Hokkaido planned to resume the operations of the bullet train from noon. He was also trying to resume other rail services on Friday afternoon, a spokesman said.
However, manufacturers were still affected by power outages.
The Tomakomai factory of Toyota Motor Corp, which manufactures transmissions and other parts, said the operations remained suspended indefinitely until the power was restored, a spokesman said.
Toppan Printing's operations at a plant in Chitose, which manufactures food packages, will remain suspended until it regains power, a spokesperson said.
Cultural events were also affected, with a football match between Japan and Chile scheduled for Friday in Sapporo suspended.