A rescue helicopter crew managed to save one of the people in distress following the shipwreck.
An Egyptian citizen was rescued, a coast guard spokeswoman told the Associated Press.
The Raptor freighter sent out a distress signal late on Saturday night then sank for reasons that remain unclear.
It was reportedly carrying salt.
The Comoros-flagged ship was bound from Egypt to Istanbul, according to maritime website Marinetraffic.com.
Its crew came from Syria, India and Egypt.
A Greek navy frigate and three coast guard boats took part in the large-scale rescue operation, Greek media reported.
A severe storm has been raging throughout southeastern Europe since Saturday.
Northwesterly winds in excess of 80km/h are blowing in the area, Greece's weather service said.
Almost all ferry connections between the Greek islands and the mainland have been cancelled.
with AP
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