Admiral Damian Carlos, the Philippine coastguard's commander, said seven people were receiving treatment for injuries.
He said authorities were still investigating the cause of the fire.
Rod Terilla, 39, who survived with burn wounds, said: "We saw smoke billowing from the storage room of the ship, then the fire quickly spread to the second floor and then to the rest of the ship so we immediately put on our life jackets and jumped into the water."
He said the ship was almost gutted, with only its wooden hull floating on the water by the time survivors were ferried away from the site by passing motor boats.
The Philippines' worst ferry disaster occurred in the 1990s when a ferry collided with an oil tanker and killed about 5,000 people.