Prime Minister Yasuo Fukuda said the government was mobilizing troops, police and "everybody we possibly can" to find the missing and rescue and treat the injured.
"Our most important task is to save as many lives as possible, and we are doing the best we can," he said.
The force of the quake, which was followed by 153 aftershocks, buckled countless roads, including one highway that was severed when a stretch of land collapsed, creating a cliffside. Electricity was cut to about 29,000 households and water to about 500 others, though services were mostly restored by Saturday night.
At a nuclear power plant in Fukushima, the jolt splashed 5 gallons of radioactive water from two pools storing spent fuel, operators said. Trade and Industry Ministry official Yoshinori Moriyama, however, said there was no leakage outside the plant.
The three dead included a man who ran out of a building in fear and was hit by a passing truck, another man buried in a landslide while fishing, and a construction worker who was hit by a falling rock at a dam, officials said.
The 8:43 a.m. quake was centered in the northern prefecture (state) of Iwate, and was located about 5 miles underground -- revised from an initially estimated depth of 6.2 miles 10 kilometers. It was felt as far away as Tokyo.
"It shook so violently that I couldn't stand still. I had to lean on the wall," said Masanori Oikawa, an Oshu city official who was at home near the epicenter when the quake struck. "When I rushed to the office, cabinets had been thrown onto the floor and things on the desks were scattered all over the place."
The quake also knocked down equipment and car parts at the Iwate factory of Kanoto Auto Works Ltd., a Toyota Motor Corp., subsidiary that assembles popular Corolla and other models, company spokeswoman Seiko Watanabe said. The company has not decided whether to resume production Monday.
A semiconductor subsidiary of Fujitsu Ltd. halted production "as a precaution" but there was no major damage to the building or equipment, company spokesman Yasuhiko Youdou.
Rescuers said their top problem was the fractured road system, which stopped them from reaching isolated hamlets in the damage zone. Hundreds of people in several isolated towns with disrupted roads were waiting for rescuers to arrive.
"We're getting growing reports of damage, but we can't even get out there to assess the situation with roads closed off because of landslides," said Norio Sato, a city official in one of the hardest-hit towns, Kurihara.
In that town, a landslide buried 15 construction workers. Twelve managed to dig themselves out, but three were still missing. Four people at Komanoyu hot springs were also missing after a separate landslide hit the resort, said another city official, Katsuyuki Sato.
Nearly nine hours after the quake hit Kurihara, Marue Supermarket manager Kikuchi Kazuya was still cleaning up amid fear of aftershocks. "A lot of liquor bottles fell on the floor," he said, adding that he has kept the store open for customers who need supplies. The quake "was really scary, and I'm worried as we continued to feel many aftershocks."
The Defense Ministry dispatched a dozen helicopters and patrol aircraft to the region to conduct flyovers and assess the extent of damage. The government also sent a CH-47 helicopter carrying Disaster Minister Shinya Izumi to the region.
Local governors were asking for more troops.
Footage shot from media helicopters showed landslides on rural roads running along knots of mountains separated by long stretches of rice fields. Footage aired on national broadcaster NHK also showed a bridge that collapsed. NHK said four people were seriously injured while riding on a bus over a bridge when the quake hit, but it was unclear whether it was the same one.
Footage from the closest large city, Sendai, showed the force of the quake shook surveillance cameras for 30 seconds. Still, Sendai appeared largely unscathed.
"So far we have not received any reports of damage or injuries. Everything is normal," Hideki Hara, a police official in Sendai, told the AP. "Phone lines, water and electricity are all working right now."
Japan is one of the most earthquake-prone areas in the world. The most recent major quake in Japan killed more than 6,400 people in the city of Kobe in January 1995.
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