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.
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It has been reported that mobile phone systems in crete were temporarily overloaded in the immediate aftermath of the quake as a result of demand on the network.
The island is located within a seismically active area.
A number of small earthquakes have been recorded on the popular tourist island in recent years.
Earlier this year, a 4.8 magnitude earthquake hit in the sea near Crete, according to the Geodynamic Institute of the National Observatory of Athens.
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