Local fishermen joined five coastguard vessels, a helicopter and divers in rescue operations early on Monday.
Officials said 90 people had been rescued and that 31 of them were injured and being treated in hospitals.
"Our rescue operations are continuing [for the missing people] around the area where the boat sank, but because of the darkness of night it's been difficult to work," Selahattin Hatipoglu, governor of Balikesir province, said.
The cause of the sinking was not immediately known.
Passengers said the ship sank in about 15 minutes and that many of those on board were asleep in their vehicles when it began to go down.
"The ship was rocking back and forth, to the left then to the right, then finally sunk, completely sunk," according to one survivor.