Houses in the town were hit by landslides, and one report said five residents were found with no vital signs.
A powerful quake rocked Japan's northernmost main island of Hokkaido early Thursday, triggering landslides that crushed homes, knocking out power and forcing a nuclear power plant to switch to a backup generator.
In the Hokkaido quake, more than 20 houses were flattened in Atsuma and Abira after mountain slopes collapsed over them across wide areas, leaving vegetation only on the mountain ridges.
Government spokesman Yoshihide Suga said two people had been killed, with local media reported around 40 were missing. The number missing had earlier been put at 19. The collapsed remains of what appeared to be houses or barns were scattered about.
It had been hoped that power would be restored in hours and some electricity gradually returned but damage to generators at the plant means it may take more than a week before it is back up, Mr Seko said. Buses and trains were also halted.
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.
The quake hit just two days after Japan experienced another natural disaster - TyphoonJebi, the strongest storm to hit the country in 25 years.
Kansai International Airport has been shut since Typhoon Jebi ripped through Osaka on Tuesday, although some domestic flights operated by Japan Airlines (JAL) (9201.T) and ANA's (9202.T) low-priced carrier Peach Aviation resumed on Friday, the carriers said.
Japan's Meteorological Agency said the quake's epicenter was 40 kilometers (24 miles) deep.
The central government set up a crisis management taskforce at the prime minister's office. Over 120 people were injured, while dozens more feared missing under collapsed structures. Spent fuel in storage pools was safely cooled on backup power that can last for a week, the agency said.
Japan's industry minister, Hiroshige Seko, has instructed Hokkaido Electric to restart its biggest coal plant after the station was tripped by the quake.
Farming, tourism and other services are big economic drivers on Hokkaido, which accounts for just 3.6 percent of Japan's gross domestic product, but there is some industry.
National broadcaster NHK aired footage of the moment the quake struck Muroran, with its camera violently shaking and all city lights going out a moment later. Agency official Toshiyuki Matsumori, at a early morning news conference, warned residents to take precautions for potential major aftershocks in coming days.
The Yomiuri ShimbunPower was restored at about 1.4 million households, or almost 50 percent of all affected homes across Hokkaido, as of 10 a.m. Friday after a powerful quake the previous day.
Officials say about 30 people are unaccounted for.
Houses destroyed by the landslide in Atsuma town.
The station was closed after the devastating natural disaster and tsunami that hit Japan in March 2011, causing the meltdown of three reactors in the Fukushima Daiichi Nuclear Power Plant complex.
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