The death toll from a ferocious typhoon in the Philippines climbed to 54 on Thursday, as home-wrecking floods shifted downstream to coastal villages, displacing tens of thousands of residents.

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.

Close to 60,000 people left their homes in Bulacan and Pampanga, a geographic catch basin for waters from the upland provinces of Nueva Ecija and Aurora, which bore the brunt of Koppu on Sunday and Monday.

Lontoc said the floods in the coastal areas may last a week.

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.

A report from the national disaster monitoring office said close to 500,000 people had been displaced by 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 on Wednesday, 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 on Wednesday.

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.

Koppu had weakened into a low pressure area on Thursday, bringing moderate rains over the outlying Batanes islands in the far north of the Philippines, state weather forecaster Gener Quitlong told AFP.

The Philippines is battered by an average 20 typhoons a year, many of them deadly.

In November 2013, 7,350 people were left dead or missing after the most powerful storm on record, Haiyan, wiped out entire communities in the central islands.