Rescue teams resumed their search for survivors Friday after a ferry carrying more than 250 passengers capsized off Quezon province Thursday, with at least five confirmed dead.
The accident occurred in rough waters off Infanta town as the Mercraft 3 keeled over en route to Polillo Island.
The 206-tonne vessel had been given the green light to sail as Tropical Storm "Vinta" (international name: Tembin) gathered pace over the southern Philippines nearly a thousand kilometers away, as there were no storm alerts in the local area, the Philippine Coast Guard (PCG) said.
But a survivor told local radio that the ferry was forced to stop at sea due to large waves and strong winds before it started taking in water from the bow and tipped over.
Filipino ferries, which seasonally brave rough seas in the Pacific typhoon belt, are notorious for overloading.
Some 252 people have so far been pulled to safety, with the death toll up to five.
The PCG had earlier said only 251 passengers and crew were on board but confirmed the vessel had a 286-person capacity.
Officials gave no explanation for the discrepancy but acknowledged the boat had carried more than the 251 people listed on its manifest.
Rescuers are yet to determine how many are still missing, said Efren Ritual, an Infanta rescue official.
"The search will continue because there are still people here looking for their missing relatives," he told AFP by telephone.
Local fishing boats and the Philippine Navy were assisting in the search, according to the PCG office in Manila.
Malacañang said Friday it is "saddened by the unfortunate incident" and called on transportation officials to exercise greater vigilance amid the "expected huge influx of travelers to the provinces this holiday season."
The Philippines, an archipelago of more than 7,000 islands, is plagued by poor sea transport, with its badly regulated boats and ships prone to overcrowding and accidents.
The world's worst peacetime disaster at sea occurred in Philippine waters in 1987, when ferry MV Doña Paz collided with an oil tanker in a pre-Christmas accident south of Manila that claimed more than 4,000 lives.