Around 1.6 million households in the sparsely populated northern island of Hokkaido were still without power after the quake damaged a thermal plant supplying electricity to the region.
Public broadcaster NHK said the death toll had doubled to four and that six people were found in cardiopulmonary arrest, a term commonly used in Japan before death is formally confirmed.
Suga said authorities were doing their utmost to rescue and assess damage after receiving hundreds of calls about people missing and buildings collapsing.
Aerial views showed dozens of houses destroyed at the bottom of a hill that was engulfed by a landslide, with a rescue helicopter winching a resident to safety. The government will send 20,000 more to the affected sites, he said.
Much of the damage was done by landslides destroying houses and cutting power lines
The quake hit at 3:08 a.m., with the epicenter in the eastern Iburi district that stretches along the southwestern coast.
The Japan Meteorological Agency said that more bad weather could be on the way for Hokkaido and urged people to be vigilant for landslides, high tides and heavy rain. Smaller aftershocks have continued in the prefecture.
Another man, 82, in Tomakomai was showing no vital signs after he fell down stairs at his home. Around 130 people had sustained minor injuries, it said. At least 20 other people were injured in nearby towns, though their conditions were not immediately known.
Rescuers were rushing to unearth survivors and restore power Thursday after a powerful quake jolted Japan's northernmost main island of Hokkaido, buckling roads, knocking homes off their foundations and causing entire hillsides to collapse. Three other outlying airports on Hokkaido were said to be operating. Kirin Brewery and Sapporo Breweries both said factories were shut by the power outage. Authorities believe it could take up to a week to fully restore power on the island. But all three reactors were not operating at the time. About 30 people were unaccounted for, disaster officials said.
There were no radiation irregularities at the plant, Suga said, citing the operator.
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Hokkaido Railway Co. suspended operations on all lines from the scheduled start of runs on the morning of September 6.
JR Hokkaido planned to resume bullet train operations from midday.
The blackout, the largest since the 1995 Great Hanshin Earthquake caused one affecting some 2.6 million households, also affected around 80 hospitals, as well as telephone services and television broadcasts in Hokkaido.
New Chitose Airport also restarted services for domestic flights to and from the main gateway to Hokkaido, although many people were unable to secure seats.
The quake triggered landslides that crushed homes in Atsuma.
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Many roads were closed and some were impassable.
Massive landslides altered the landscape of some mountain ranges in the quake-hit area.
Officials warned of the risk of further quakes.
A fire broke out at a steel plant operated by Mitsubishi Steel Manufacturing in the city of Muroran, but has largely been brought under control, a spokesman told Reuters.
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