Rescuers have saved at least 316 passengers.
The M/V Trisha Kerstin 3, an inter-island cargo and passenger ferry, was sailing from the port city of Zamboanga to southern Jolo island in Sulu province with 332 passengers and 27 crew members when it apparently encountered technical problems and sank after midnight on Monday, coast guard officials said.
The ferry sank in good weather about a nautical mile (nearly two kilometres) from the island village of Baluk-baluk in Basilan province, said coast guard Commander Romel Dua.
"There was a coast guard safety officer on board and he was the first to call and alert us to deploy rescue vessels," Dua said, adding that the safety officer survived.
One of the rescued passengers, Mohamad Khan, said the ferry abruptly tilted to one side and took on water, hurling people including him and his wife, who was holding their six-month-old baby, into the sea in the darkness.
He and his wife were rescued, but their baby drowned.
"My wife lost hold of our baby and all of us got separated at sea," a distraught Khan told a volunteer rescuer, Gamar Alih, who posted a video of Khan's remarks on Facebook.
Alih, a village councilor from Zamboanga city, told The Associated Press he volunteered to help in the search and rescue because some of his relatives were among the ferry passengers. They all survived.
Coast guard and navy ships, along with a surveillance plane, an air force Black Hawk helicopter and fleets of fishing boats were carrying out search and rescue operations off Basilan, Dua said.
The coast guard said 316 passengers had been rescued and at least 15 bodies found.
The cause of the ferry sinking was not immediately clear and there will be an investigation, Dua said, adding the coast guard cleared the ferry before it left the Zamboanga port and there was no sign of overloading.
Sea accidents are common in the Philippine archipelago because of frequent storms, badly maintained vessels, overcrowding and spotty enforcement of safety regulations, especially in remote provinces.
In December 1987, the ferry Dona Paz sank after colliding with a fuel tanker in the central Philippines, killing more than 4300 people in the world's deadliest peacetime maritime disaster.
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