The quake was at a depth of 80 km (49.71 miles), EMSC said.
It measured 5.5 on the Richter scale and hit 60km (37 miles) to the northeast of Siteía, the independent monitoring organisation reported.
The tremor prompted authorities to issue a tsunami warning and urge residents to take care.
People have been warned to move away from the coast and reach a higher place.
The earthquake is reported to have been felt as far away as north Africa.
No injuries or damage to buildings has been reported in any of the areas affected.
A warning message tweeted by the EMSC advised those next to the sea to “move away from the coast and reach a higher place”.
No such message has yet been broadcast by Greek authorities.
The earthquake is reported to have been felt as far away as north Africa. No injuries or damage to buildings has been reported in any of the areas affected.
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