According to the US Geological Survey the quake had a 6.4 magnitude, while the Athens Observatory gave it a magnitude of 6.2.
The epicentre was some 60 kilometres off the city of Hania in western Crete, the state-run Athens News Agency said.
The earthquake struck at 4:11pm (1311 GMT) and its epicentre was in the sea, 275 kilometres south of Athens, the observatory said, describing the quake as "strong."
"It was very impressive because the shaking lasted some 40-50 seconds," a woman who identified herself only as Vassia, said.
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According to the Athens News Agency, life in Hania returned to normal a few hours after the quake, which had initially sent people rushing into the streets in panic.
Shops and houses suffered minor damages and local television showed images of items falling off supermarket shelves.
According to Skai radio station, an elderly person was lightly injured while attempting to jump out a window.
Yesterday, a 4.4-magnitude earthquake, described as "mild" by the observatory, struck the north of the country causing no damage.