Near the epicenter, landslides wiped out houses in the tiny town of Atsuma, home to 40 residents.
The majority of the dead are from the small rural town of Atsuma, where a cluster of dwellings were wrecked when a hillside collapsed from the force of the 6.6-magnitude quake, causing deep brown scars in the landscape. After a long, dark night a large share of the lights were back on early Friday in the prefectural capital of Sapporo, a city of 1.9 million.
It struck near Hokkaido's main airport, New Chitose Airport, which would be closed for at least Thursday.
At least nine people were killed, Prime Minister Shinzo Abe said.
In June, a deadly tremor hit Osaka region, killing five and injuring more than 300 people.
Prime Minister Shinzo Abe said almost half of the almost 3 million households on the island had their power restored after a day of island-wide blackouts.
Transports were also badly affected, as all trains across the island were halted.
Public broadcaster NHK reported the first confirmed fatality and said 120 people had also been injured after the 6.7-magnitude quake. At least 20 other people were injured in nearby towns, though their conditions were not immediately known.
In Atsuma, a town of 4,600 people, 26 were still unaccounted for.
Eight people are reported to have died, according to local media, while there are around 40 now missing. It may take a week to restore power fully to all residents, he said.More news: Tiger Woods calls Nike's Kaepernick campaign a 'beautiful spot'
Around 1.6 million homes on Hokkaido remained without power on Friday, after the 6.7-magnitude quake damaged a thermal plant that caters to the region.
After the Tomari Nuclear Power Station in Hokkaido suffered a power outage, authorities started cooling its fuel rods using emergency power, Chief Cabinet Secretary Yoshihide Suga said.
There were no radiation irregularities at the plant, Suga said, citing the operator.
Three nuclear reactors were offline for routine safety checks at the time, but are now running on backup generators.
The powerful quake and tsunami in March 2011 that hit northerneast Japan destroyed both external and backup power to the Fukushima Dai-ichi nuclear plant, causing meltdowns.
The death toll from a powerful natural disaster that rattled the northern Japanese island of Hokkaido doubled to at least 16, Prime Minister Shinzo Abe said on Friday, with more than half the island's 5.3 million residents still without power. The company said it can not update information on the social media due to the blackout.
Japan's economy minister says damage from a powerful quake at the main thermal plant has delayed the restoration of power on the main northernmost island of Hokkaido for more than a week.
According to the US Geological Survey, the quake struck around 68 km southeast of Sapporo. The utility aimed to raise that number to 2.4 million, or over 80 percent, by the end of Friday, industry minister Hiroshige Seko said.
"No changes to the schedule are planned", he said. Power was knocked out across the island.
The lack of power generated chaos throughout the island, when emergency services are still digging in the rubbles looking for survivors.