Officials said ten passengers had been rescued, but accounts differed as to how many people were on board the boat, which was carrying migrants from Turkey to Greece.
At least 11 people, some of them children, had already been found dead.
Greece draws criticism
The news comes shortly after the EU criticized Athens for its handling of the migrant crisis in a newly issued report.
An EU investigation said on Wednesday it had found major flaws in the country`s border management, insisting that Athens had neglected its obligations to prevent the thousands of migrants from crossing into Europe from the Mediterranean.
A Greek government spokesperson said it was unwise of Brussels "to try to create a mood isolating Greece," according to the Associated Press.
Around 46,000 people have arrived in Greece in January, according to the UN. At least 170 people have already been killed attempting the journey.
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