Police simultaneously raided three underground workshops in the port city of Izmir on Friday, seizing 49 boats that failed to meet safety standards, the official Anatolia news agency said.
The boats were destroyed by the police, it said, adding that the workshops now faced closure.
Turkey is home to at least 2.2 million refugees from Syria's civil war.
It has become a hub for migrants seeking to move to Europe, many of whom pay smugglers thousands of dollars for the risky crossing to Greece.
After the deal, Turkey appears to have stepped up efforts, stopping boats, rounding up scores of suspected smugglers and seizing hundreds of sub-standard life jackets given to the refugees.
German Chancellor Angela Merkel is to visit Ankara on Monday to discuss implementation of the deal.
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