The captain of the ferry MV Thomas Aquinas ordered the ship abandoned when it began listing and then sank just minutes after collision late Friday with the MV Sulpicio Express Siete, coast guard deputy chief Rear Adm. Luis Tuason said.
Transportation and Communications Secretary Joseph Abaya announced official passenger figures following confusion over the actual number of people on the ferry.
He said the ferry carried 831 people — 715 passengers and 116 crew — fewer than the numbers given earlier by the coast guard and ferry owner, 2Go. He said the death toll has risen to 31 with 629 rescued.
There were foreigners on board "but they are all OK," except for a New Zealand citizen who was in a hospital, Abaya said.
Cebu coast guard chief Cmdr. Weniel Azcuna said 171 were listed as missing, but the figure would go down once the number of crew members who have been rescued are officially accounted.
Tuason said some of the missing could still be trapped inside the vessel that sank in waters about 33 meters (100 feet) deep off Talisay city in Cebu province, 570 kilometers (350 miles) south of Manila.
Tuason said navy divers recovered at least four bodies early Saturday. Reporters at the site, about two kilometers (1.25 miles) from shore, saw the bodies coated with fuel and oil that spilled from the ferry.
In a statement, 2Go said the ferry "was reportedly hit" by the cargo vessel "resulting in major damage that led to its sinking." An investigation will begin after the rescue operation, the coast guard said.
Abaya said the cargo vessel smashed into right side near the rear of the ferry which was coming from Nasipit in Agusan del Sur province in the southern Philippines and making a short stop in Cebu before proceeding to Manila.
"I guess it hit the ferry at a very vulnerable point, probably at its water line or below the water line so that it did not take long for it to sink," he said.
One of the survivors, Jenalyn Labanos, 31, said the ferry quickly tilted to its side after the impact and sank about 20 minutes later.
She said the crash threw her and two companions to the floor of a ship restaurant followed by the lights going out.
"People panicked and the crew later handed out life vests and used their flashlights to guide us out of the ship but they could not control the passengers because the ship was already tilting," she said.
She said she suffered bruises on her hands and feet as she grabbed a rope on the side of the vessel before jumping into the water.
"I just thought to myself that I have to survive this. I left everything, my bag, my money and my passport," she said. She was headed to Manila for a flight to Dubai where she has been hired as a maid.
Accidents at sea are common in the Philippine archipelago because of frequent storms, badly maintained boats and weak enforcement of safety regulations.
In 1987, the ferry Dona Paz sank after colliding with a fuel tanker in the Philippines, killing more than 4,341 people in the world's worst peacetime maritime disaster.
In 2008, the ferry MV Princess of the Stars capsized during a typhoon in the central Philippines, killing nearly 800 people.
Survivors said many of the passengers were asleep at the time of the accident, while others struggled to find their way in the dark.
Rolando Manliguis was watching a live band when "suddenly I heard what sounded like a blast. ... The singer was thrown in front of me." He said he rushed to wake up his wife and their two children but the water was rising fast.
"When the boat was on its side, the water level was here," he said, pointing to his neck.
He said they roped down the side of the ferry into the sea and were put on a life raft.
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