Thousands of Filipinos have shovelled muck and debris from flood-ravaged homes, shops and roads under a shining sun after nearly two weeks of non-stop rain shut down the capital and forced hundreds of thousands to flee from the deluge.

At least 49 people died and more than two million people were affected by Manila’s worst flooding since 2009.

More than half of the sprawling metropolis of 12 million was submerged at the peak, and schools and offices have been closed for days.

Under a hot sun on Thursday as the rain finally stopped, residents began to fix dishevelled homes and stores in flood-hit communities that resembled a wasteland littered with mud-caked garbage.

Some of the displaced in the still-crowded evacuation centres have begun to trickle back to the neighbourhoods where floodwaters have subsided, Social Welfare Secretary Dinky Soliman said, but more than 314,000 people remained in the hundreds of evacuation centres in Manila and outlying provinces.

“We were totally washed out,” said Rudy Aquino, a flower shop owner along Araneta Avenue, where more than three metres of rampage floodwaters swamped everything and carried all sorts of garbage and even a wayward cargo truck.

Aquino, whose shop also was hit by the more massive flash flood in 2009, told The Associated Press he was moving to a safer location when the deluge engulfed his business on Tuesday and again late on Wednesday when flood waters rose again.

As he tried to rise from the latest onslaught, a fresh supply of red orchids arrived at his shop on Thursday as he and the staff were cleaning up.

Even though the weather has cleared, the government was busy with rescue and relief work in the worst-hit areas, especially along swollen rivers and coastal communities.

In hard-hit Marikina city in the capital, rescuers in rubber boats floated down still-flooded streets to reach thousands of residents marooned in submerged houses along the Marikina River.

After the rains stopped, thousands of shoppers descended on grocery stores to stack up on food and other supplies.

The death toll jumped to 49 late on Thursday after casualty reports from the provinces reached the Civil Defence Office. Most were drowning victims. At least six were missing.