The magnitude-6.3 quake left some homes with rooftop tiles broken and cracked walls, while goods fell off store shelves, according to the Meteorological Agency and Japanese TV news footage.
The agency had earlier said the magnitude was 6, but later upgraded it.
The quake was centred on Awaji Island, just south of Kobe, at a depth of 15 kilometres.
The quake was in the area, where a magnitude-7.2 quake killed more than 6,400 people in 1995.
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