Prime Minister Shinzo Abe said 25,000 self-defence force troops were being deployed for rescue operations.
A magnitude 6.6 quake rocked Japan's northernmost main island of Hokkaido early Thursday.
It was the first time since the utility was established in 1951 that had happened. So far, power has been restored to roughly 1,455,000 homes, or about half of the total in the prefecture. However, damage to generators at the plant meant that a full restoration of power could take more than a week, Seko said.
"We send our deepest condolences and sincerest sympathies to those affected by the quake that struck the central-eastern part of Iburi region in Hokkaido", a statement read.
Some streets were cut off by downed trees, and additional images from the broadcaster showed crumbled buildings.
But amid continuing power shortages, he urged citizens to conserve energy by using fewer lights in shops and restaurants and "for example family members staying together in one room". "I will live my life remembering that", he told Hokkaido Cultural Broadcasting.
Hokkaido's main aviation hub, New Chitose Airport, was reportedly shut for at least Thursday.
Atsuma resident Tenma Takimoto told local media that his 16-year-old sister, father and grandmother were caught in the landslide.
11am: A powerful quake hit wide areas on Japan's northernmost main island of Hokkaido this morning triggering landslides as well as causing the loss of power at almost all of 3 million households and a nuclear power plant to go on a backup generator. Mandatory credit Kyodo/via REUTERS.
High winds smashed a tanker into a bridge, forced one of the country's largest airports to close and left at least 10 people dead. Roof tiles and water lay on terminal floors. More than 200 flights and 40,000 passengers would be affected, Kyodo News agency said.
Japan is still recovering from the worst typhoon to hit the country in 25 years, which struck the western part of the country on Tuesday, claiming at least 11 lives and causing major damage to the region's main airport.
Kansai International Airport in western Japan has been shut since Typhoon Jebi ripped through Osaka on Tuesday, although some domestic flights operated by Japan Airlines Co Ltd and ANA Holdings Inc's low-priced carrier Peach Aviation resumed on Friday, the carriers said.
Japan is in the midst of a record tourism boom and will host the Olympics in 2020. Kirin Brewery and Sapporo Breweries both said factories were shut by the power outage. Residents were warned to take precautions.
Soldiers in fatigues and orange-clad rescue workers searched for survivors, picking through debris on huge mounds of earth near the epicenter in Atsuma in southern Hokkaido.
Japan, situated on the Ring of Fire arc of volcanoes and oceanic trenches that partly encircles the Pacific Basin, accounts for about 20 per cent of the world's earthquakes of magnitude 6 or greater.
The 2011 quake and tsunami in northern Japan destroyed both external and backup power to the Fukushima Dai-ichi nuclear plant, causing meltdowns.
Emergency power was cooling spent fuel at the Tomari Nuclear Power Station, which has been shut since Japan's 2011 Fukushima natural disaster and tsunami.