Inundations from torrential weekend rains in mountain regions caused by Typhoon Koppu cascaded into coastal fishing and farming villages, submerging them in waters up to three metres (10 feet) deep, officials said.
Residents of Bulacan and Pampanga province, around two hours' drive from the capital Manila, fled by foot to evacuation centres as the waters rose quickly overnight, aggravated by a high tide, they said.
"The waters have nowhere else to go. Imagine two to three days worth of rain from the mountains coming down," Nigel Lontoc, assistant director of the region's civil defence office, told AFP.
Lontoc said the floods in the coastal areas may last a week.
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Koppu made landfall on the east coast of Luzon, the Philippines' biggest and most populated island, early Sunday with 210-kilometre (130-mile) per hour winds.
Koppu, the second strongest typhoon to hit the disaster-weary country this year, then crawled over vast swathes of Luzon for three days, bringing torrential rains that triggered landslides and massive flooding.
The waters had receded considerably in the upland provinces and many had returned to their mud-covered homes.
But the death toll climbed to 54, from 47 yesterday, based on an AFP tally of confirmed figures from national and local authorities.
In the Cordillera mountain region, the civil defence office confirmed five more deaths from landslides on Monday and Tuesday, raising the death toll to 21 from 16 yesterday.
In the central farming regions of Luzon, the deaths of two 12-year-old girls were reported, one of whom died from drowning and the other from a snake bite, according to the regional civil defence office.
The Philippines is battered by an average 20 typhoons a year, many of them deadly.