Philippine disaster officials were shifting Friday from rescue work to a massive cleanup of the capital following nonstop rains that left tonnes of muck and debris from floods littering the city.

The torrential monsoon rains that began Sunday left at least 60 people dead in the worst flooding in Manila since 2009. More than half of the sprawling metropolis of 12 million was submerged at the peak of the floods, and schools and offices closed for days.

About 2.4 million people in Manila and nearby provinces have been affected, forcing more than 360,000 to seek shelter in government-run evacuation centres, the Office of Civil Defence reported Friday.

The sun was out for a second day Friday, and residents were hard at work fixing dishevelled homes and stores in flood-hit communities that resembled a wasteland covered with mounds of mud-caked garbage.

"It's really an eyesore when we saw it from the helicopter," said civil defence chief Benito Ramos. "There will be no more rescue. It's now 'Operation Cleanup."'

He said soldiers will be mobilized to help local authorities collect the debris that have clogged streets and waterways.

Some of the displaced in still-crowded evacuation centres have begun to trickle back to their communities, where floodwaters have subsided, Social Welfare Secretary Dinky Soliman said.

Reservists will be assigned to help repack relief supplies for people still in emergency shelters, Ramos said.

North of the city, rains still poured intermittently and a helicopter carrying President Benigno Aquino III had to land on an isolated portion of a highway early Friday when visibility became difficult, said his spokesman Ricky Carandang.

No one was hurt and the presidential party proceeded by car to visit flood victims in his home province of Tarlac, Carandang said.

The death toll from the floods rose to 60 early Friday after casualty reports came in from more provinces, Ramos said. Most were drowning victims. At least seven were missing.

Of the total killed, 26 were from metropolitan Manila, including nine killed in a landslide in suburban Quezon City.