Greece was using a helicopter, three patrol boats and a navy vessel to look for other survivors after 19 people were rescued.
"Two bodies were recovered by the Greek coastguard and another three by the Turkish coastguard," a Greek coastguard spokeswoman said.
"The search continues to find another 13 people," she added.
The boat sank on Tuesday off the Greek Aegean island of Agathonissi, near the Turkish coast, and survivors told authorities between 33 and 37 people had been on board.
According to UN figures, some 137,000 migrants risked their lives to cross the Mediterranean in the first six months of the year, mostly fleeing conflict.
This was 83 per cent higher than the first half of last year.
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