'Based on the manifest of the ship, only two persons are unaccounted for,' he said. 'We are continuing to search for the two missing.'
The Superferry 9 sank after listing for several hours.
Tamayo said an investigation would be conducted to determine the cause of the accident, but initial reports said the ship had problems with its generator.
Sea travel is a major mode of transportation in the Philippines, an archipelago of more than 7,000 islands.
In June 2008, a passenger ferry sank off the central Philippines at the height of Typhon Fengshen, drowning more than 800 passengers.
The country was the site of the world's worst peacetime shipping disaster in 1987, when more than 4,000 people perished in a collision between the ferry Dona Paz and an oil tanker off the central island of Mindoro just before Christmas.