A passing cargo ship rescued 18 people from the same boat, which was about 28 kilometres from Crete. The circumstances surrounding the 12 deaths are unclear, according to the Greek coastguard.
Eight more people were recently found dead on another boat.
The EU border agency Frontex has also rescued more than 80 migrants from boats and taken them to a port on Crete.
Thousands of migrants have taken the dangerous sea route from North Africa, usually Libya, to the Greek archipelago in recent months.
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