The strong quake struck 82 kilometres (51 miles) northeast of Crete’s capital Heraklion, at a depth of 68 kilometres, the USGS said.
The region popular with tourists has been rattled by multiple tremors in recent months, prompting schools in Santorini and neighbouring islands to close temporarily.
Thousands of earthquakes, mainly of low magnitude, were recorded from late January between the islands of Santorini, Amorgos, Ios, and Anafi in the Cyclades group southeast of the Greek mainland.
The seismic swarm caused no casualties or significant damage.
Located where the African and Anatolian tectonic plates converge, the Aegean Sea is often hit by earthquakes.
But the region had not experienced a phenomenon of such magnitude since records began in 1964, experts said.
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