The magnitude 7.4 quake, which struck shortly before midnight on Wednesday and revived memories of the March 11, 2011 disaster, also severed transport links to the northeast, with Shinkansen bullet train service indefinitely suspended and at least one major highway to the region closed for safety checks.
Parts of Tokyo lost power immediately after the quake, though most regained it within three hours. But some 36,400 households serviced by Tohoku Electric Power Co in northeast Japan remained without electricity by 9:00 a.m. local time (0000 GMT) on Thursday, although the firm said it expected most will have supply restored later in the day.
Prime Minister Fumio Kishida said four people had died and that the government would be on high alert for the possibility of further strong tremors over the next two to three days.
The quake, initially measured at magnitude 7.3 but later revised up to 7.4 by the Japan Meteorological Agency, hit at 11.36 p.m. local time just off the coast of Fukushima prefecture at a depth of 60 kilometers. The 2011 quake and tsunami off Fukushima - commemorated across the country less than a week ago - left some 18,000 dead.
A tsunami warning was issued but canceled early on Thursday morning. Some areas reported a rise in the sea level but no serious damage was immediately reported.
The 2011 disaster also set off meltdowns at the Fukushima Daiichi nuclear power plant. No abnormalities were reported at any nuclear power plants, although authorities had earlier said a fire alarm had been triggered at a turbine building at the crippled plant.
Manufacturers were trying to gauge the potential damage to their facilities.
Renesas Electronics Corp, the world's biggest maker of automotive microcontroller chips, said it was checking for quake damage at three plants in Japan.
Meanwhile Toyota Motor Corp said it had canceled the day shift at two factories in northeast Japan after workers evacuated the plants during their evening shift on Wednesday. The automaker said it will decide on the evening shift later.
Mizuho Financial Group Inc's main banking arm said some of its ATMs temporarily stopped operations due to power outages, but that they had all been restored to service.
In an attempt to cover the area affected by the Shinkansen outage, All Nippon Airways said it had added extra flights to the northern city of Sendai. There were no forecasts of when regular rail service might be restored.
Japan's benchmark Nikkei stock average jumped, with no impact seen from the quake.