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A 9-year-old girl and two men in their 80s have been killed by a strong natural disaster in the western Japan metropolis of Osaka.

Motochika Goto, 85, was crushed by a bookcase and died in Ibaraki in the Osaka suburbs, according to local police.

Prime Minister Shinzo Abe instructed the government agencies to "swiftly collect information on damage, make utmost efforts in rescuing and saving lives".

The strongest shaking was north of Osaka, the agency said.

The Osaka prefectural government reported two deaths, and an Ibaraki city official confirmed a third.

Officials also said its focus was 13 kilometers below the surface in northern Osaka Prefecture.

Despite having a relatively low magnitude, the quake caused quite a shake, registering a lower six on the Japanese experiential scale of up to seven, meaning it is hard to stay standing.

The Japanese meteorological agency put the magnitude at 5.9, and the epicentre at a depth of 10km.

"It was not as bad as the Kobe quake", he told the Associated Press from Osaka.

"The fault has not moved in over 10,000 years and has attracted attention as a risky fault, which has prompted surveys and researches", said Toda.

"I saw the ceiling and the floor undulating, and I could barely stand".

Honda Motor Co. and Mitsubishi Motors said they were resuming operations after temporary suspensions and safety checks. More than 170,000 homes were without power as of 8:20 a.m., regional utility Kansai Electric Power Co. said. There were no reports of abnormalities at its nuclear plants in the region. National broadcaster NHK reported a wall near a school swimming pool fell on the girl.

The quake struck at 8:00 am, as platforms would have been heaving with passengers waiting to board their commuter trains to work.

Thee people have been confirmed dead after a magnitude-6.1 natural disaster struck Osaka and neighboring prefectures at 7:58 a.m. on Monday.

Monday's temblor was the latest in a string of quakes over the last few days.

A strong magnitude 6.1 quake struck the city of Osaka and the surrounding area on Monday morning.