On Monday morning coastguard aircraft scoured the waters around where the ship sank looking for survivors.
Some of the rescued passengers said the roll-on, roll-off vehicle ferry had gone down within minutes after taking in water from the bow ramp.
"It was midnight, and almost all the passengers were asleep," said 14-year-old Eric Musni.
|Survivors say the MV Baleno-9 capsized and sank within minutes [AFP]
"Then the ferry suddenly capsized. People were running everywhere, they didn't know what to do."
Another survivor, Jonathan Umali, recalled the speed at which the ship sank.
"I couldn't do anything to help my companion, Cecilia, and her daughter. All I could do was watch them drown," he said.
The sinking is the second ferry accident to hit the Philippines in less than a week.
On Thursday a ferry collided with a fishing boat in Manila Bay, leaving at least 24 missing.
Ferries are an important means of cheap transport in the Philippines, an archipelago of more than 7,000 islands.
But accidents are common because of overcrowding, poor maintenance and frequent tropical storms.
The world's deadliest peacetime maritime disaster occurred south of Manila in 1987 when the Dona Paz ferry capsized after colliding with a small oil tanker, killing more than 4,000 people.