The southwest monsoon, intensified by Typhoon Pabuk, brought torrential rains in Manila and nearby provinces of Luzon Island, killing at least 30 people.
Heavy rains triggered landslides and flash floods affecting more than 36,000 people over the past two days, officials said.
The local weather bureau has lifted the severe rainfall warning, but light to moderate rains are expected to persist until Wednesday.
Cleanup operations have begun in the heavily hit Zambales Province, about 138km south of Manila, with major roads being cleared of mud and debris.
Talent manager Alex Bangoh and his entertainment troupe were among the villagers who were trapped during Monday's severe flooding.
It's going to be a miracle if we find any more survivors.
"When we woke up, we saw that knee-high water has reached our bedroom. Within one hour, half of our house was under water, which is why we decided to crack open our ceiling and went up to our roof," he said.
At least two people drowned during heavy overnight rain, while more than a thousand families sought shelter in evacuation centres, town officials said.
Three separate landslides were reported in Subic Town during torrential rains on Monday, killing at least 18 people, officials said. Rescuers were still hoping to find survivors trapped in the landslides.
"As we see it, it's going to be a miracle if we find any more survivors, but then, we hope there will be. We will continue to look for them," said Regional disaster agency officer Bernie Tiong.
The local government declared several villages near the landslide areas as permanent danger zones and advised residents to evacuate.
Fisherman Elmer Flores was among the villagers who survived the landslide and hoped the local government would sponsor their relocation.
"We would like to leave if the government will relocate us," he said.
Monsoon rains in the Philippines have grown fiercer in recent years, with last year's deadliest monsoon submerging the capital and nearby areas, killing more than 50 people and forcing about 270,000 to seek safer ground.