Forty-six passengers and crew of the wooden-hulled ferry MV Catalyn B who were plucked alive from the water arrived before noon at the Manila headquarters of the coast guard, which alerted all vessels in the area to look for those still missing, said coast guard spokesman Armand Balilo.
A woman passenger was seen being carried on a stretcher, while others were led to a clinic for a medical examination.
The 44-feet- (13-meter-) long vessel, which was carrying 73 people on a journey from Manila to southwest Mindoro Island, sank shortly after the accident, Balilo said. The ferry had a capacity to carry 126 people and was not overloaded, he added.
All 22 crewmen of the fishing boat Natalia were safe, and their vessel did not sink after the collision off Cavite province's Limbones island, said Melvin Viola of the coast guard's operation center.
The cause of the collision at a time when millions of Filipinos were heading to their home provinces ahead of Christmas Eve was not clear. No weather disturbances were reported in the area.
Henry Tria, one of about 30 anxious relatives who flocked to the coast guard office, said five of his relatives were on board, including teenaged nephews and a 7-year-old niece who were on their way home to Mindoro.
"I told them that we should take a bigger ship but the tickets were sold out so they decided to go on this smaller ferry because they wanted to be home for Christmas," he said earlier Thursday, before the survivors arrived at the coast guard office.
It was not clear how many of his relatives have been rescued, but at least one nephew's name was on a coast guard list of rescued passengers, he added.
Sea accidents are common in the archipelago due to tropical storms, badly maintained boats and weak enforcement of safety regulations.
Last year, a ferry overturned after sailing toward a powerful typhoon in the central Philippines, killing more than 800 people on board.
In December 1987, the ferry Dona Paz sank after colliding with a fuel tanker, killing more than 4,341 people in the world's worst peacetime maritime disaster.