The death toll from the 6.7-magnitude pre-dawn quake is likely to rise as rescuers search houses buried by landslides.
About 33 people were missing and 300 were injured, public broadcaster NHK said. The number missing had earlier been put at 19.
Government spokesman Yoshihide Suga added: "I urge people in areas shaken by strong quakes to stay calm, pay attention to evacuation information. and help each other". "I thought my house would collapse".
Power was knocked out for Hokkaido's 2.9 million households.
Utilities were starting up several other thermal and hydroelectric plants and power was restored to 340,000 households, but even with those stopgap supplies thousands will still be without electricity for some time.
The quake also affected several manufacturers on the island.
Map locating the powerful 6.6 magnitude quake that hit the northern Japanese island of Hokkaido.
Airports and many roads on the island were closed and trains were idled by the power outages.
Scientists say most of that radiation quickly faded or was otherwise diluted.
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Landslides are seen in Atsuma, Hokkaido, northern Japan Thursday, Sept. 6, 2018.
Japan's Meteorological Agency said the quake's epicenter was 40 kilometers (24 miles) deep.
It is also coordinating with the Hokkaido Prefectural Government Crisis Management Division, the DFA said.
Prime Minister Shinzo Abe confirmed 16 people had been killed, many people injured, and 26 remained missing.
The idled Tomari nuclear power plant temporarily lost an external power source, forcing its operator Hokkaido Electric Power Co.to cool a spent fuel pool at its Nos.
Japan is in the midst of a record tourism boom and will host the Olympics in 2020. "I felt it went sideways, not up-and-down, for about two to three minutes", said Kazuo Kibayashi, an official in hard-hit Abira.
A fire broke out at a Mitsubishi Steel Mfg Co plant in the city of Muroran after the quake but was mostly extinguished with no injuries, a company official said. But the blackouts brought on by the quake underscore the country's heavy reliance on vulnerable power systems: without electricity, water was cut to many homes, train lines were idled and phone systems stopped in some areas.
Moments after the initial quake, an aftershock measuring 5.3 rocked the area and dozens more aftershocks followed throughout the night and into the morning.
Japan is situated on the "Ring of Fire" arc of volcanoes and oceanic trenches that partly encircles the Pacific Basin and accounts for about 20 percent of the world's earthquakes of magnitude 6 or greater.
"On behalf of Japan Football Association, I send my deepest condolences and sincerest sympathies to those affected by the powerful natural disaster that struck the central-eastern part of Iburi region in Hokkaido early this morning", JFA president Tashima Kohzo said in a statement.