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As scientists scramble to understand the cause, officials are urging residents to brace for the worst, and the rest of Japan to take this as a grim reminder of its ever-present seismic vulnerability.

The epicentre was off the coast of the Tokara island chin located in Kagoshima, almost 1,200 kilometres away from Tokyo.

An earthquake with a preliminary magnitude of 5.5 hit south-western Japan on Thursday, the Japan Meteorological Agency said.