Six of the 85 people on board the vessel have been rescued, and 40 have been reported as missing, officials said. Two of the survivors are Palestinians.
The bodies of the 43 people, all male, have been recovered. However, Turkey's Dogan news agency said the total number of fatalities was 48.
On December 8 the 15-meter (49-foot) boat, reportedly heavily overloaded, set off from the Sererihisar port to the south of Izmir. The vessel ran into rough weather and capsized.
Turkey is one of the main transit countries for illegal migrants from the Middle East to Europe. The European Union, which Turkey wants to join, has repeatedly urged Ankara to bring illegal immigration through its territory under control.