Twenty-nine more passengers are still unaccounted for, more than two weeks after the St Thomas Aquinas went down off the port of the central city of Cebu, it said in its latest report.
Rescuers were able to save 733 people after the crash, the latest in a long list of sea mishaps to hit the Philippines, an archipelago of more than 7,100 islands.
The Aquinas was passing through a narrow sealane on its way to the port of Cebu when it was hit by the freighter on August 16.
The sinking also led to an oil spill from the ferry, polluting mangrove sanctuaries, fishing grounds and beach resorts.
The leak has been plugged and authorities are looking at how to salvage the wreckage when the search is declared over.
Sea accidents are common in the Philippines, where poor safety standards and lax enforcement are typically to blame.
The country has saw the world's worst peacetime shipping disaster which occurred in December 1987 when the Dona Paz ferry collided with an oil tanker off the island of Mindoro near Manila, killing more than 4,300 people.
