Rescuers recovered 34 bodies, but as night fell they suspended the search for the 113 passengers and crew of the ferry Cebu City who were still believed missing. The search was to resume at first light.
"I think they are dead. If they were alive the fishermen should have found them already," coast guard spokesman Jaime Daquilanea said. "I think they are with the ship below."
Frogmen who located the vessel in less than 30 meters of water at the mouth of Manila Bay said they could see bodies pinned under baggage and debris.
Diver Hermogenes Guilaran said the vessel was lying on its side on the seabed, and he saw bodies trapped against the bulkheads inside the hull.
The ferry accident, the worst to hit the Philippine shipping industry since 1988, happened before dawn as the Cebu City headed out of Manila Bay. The ferry's owners said the vessel was struck by the Singapore-flagged container ship Kota Suria.
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