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The official death toll from last weekend's disaster, which swept away shantytowns built near major rivers, has exceeded a thousand but some authorities said hundreds more people could be missing and may never be found.
Benito Ramos, the civil defence chief, told AFP that coast guard and navy vessels have been drafted in for a huge rescue effort to find bodies floating amid debris up to a hundred kilometres (62 miles) away.
"By this time, there will be no survivors, just dead bodies," he said after tropical storm Washi brought heavy rains that spawned flash floods, overflowing rivers and mudslides that buried bodies or swept them into the sea.
Ramos put the death toll at 1,010 while his agency, the National Disaster Risk Reduction and Management Council, put the number of missing at 51.
However, Mayor Lawrence Cruz of the hard-hit port of Iligan said that in his city alone, more than 400 residents had been reported missing, with another 283 confirmed dead.
"We could only assume they are dead already. There is so much mud that has to be cleared up and maybe the missing are buried deep inside," Cruz said.
Philippine Red Cross chief Gwendolyn Pang said that at least 900 bodies have been recovered and confirmed that some 400 people have been reported missing.
However, she said the exact toll may never be known as some of those reported missing may in fact be among the dead, and there could be many more whose disappearance was never reported.
"Many will never be found and we don't know how many are really missing. No one will report them because entire families were swept away," Pang added.
Iligan and the larger nearby port of Cagayan de Oro accounted for most of the confirmed deaths so far.
A navy vessel recovered 11 badly decomposed bodies off the coastal town of Salay on Wednesday, navy spokesman Lieutenant-Colonel Omar Tonsay told AFP.
"Recovering bodies at sea is difficult because of the sheer volume of debris. You have to ram logs and risk holing your hull or entangling your propellers," Tonsay added.
Ramos said the maritime search could continue for two more weeks, but warned that many bodies may have sunk underwater and would never be found.
The main priority now is finding permanent shelter for the 309,000 people displaced by the floods, particularly the more than 43,000 housed in cramped evacuation centres, he said.
Health officials have warned of the risk of epidemics breaking out at the camps, which remain without proper water supply and sanitation.
Many of those in the evacuation centres are forbidden from returning home as the flood-prone areas have been identified by government as too dangerous for human habitation.