At least 47 people were killed, mostly by drowning, in Rizal province, east of Manila, radio reports quoted the local governor as saying.
Eleven more people were killed by collapsing walls and rising floodwaters in the capital area, disaster officials said.
Chief government weather forecaster Nathaniel Cruz said 42.4cm of rain fell on Manila in just 12 hours yesterday, more than the 39.2cm average for the entire month of September.
The government declared a "state of calamity" in metropolitan Manila and about two dozen storm-hit provinces, said defence secretary Gilberto Teodoro, who heads the National Disaster Coordinating Council. That allows officials to withdraw emergency money for relief and rescue.
President Gloria Macapagal Arroyo had to take an elevated commuter train to the disaster council office to preside over a meeting because roads were clogged by vehicles stuck in the floodwaters.
Two people were reported killed in suburban Muntinglupa and three others in Quezon city, said deputy presidential spokesman Anthony Golez.
The mayor of Cainta in nearby Rizal province, who was stranded atop a dump truck on a road that was neck-deep in water, told a television channel by phone that many residents climbed onto roofs to escape.
"The whole town is almost 100% underwater," mayor Mon Ilagan said. About 34.1 cm of rain fell on metropolitan Manila in just six hours, close to the 39.2cm average for the entire month of September. The previous record was 33.4cm recorded during a 24-hour period in June 1967, chief government weather forecaster Nathaniel Cruz said.
"However good your drainage system is, it will be overwhelmed by that amount of rainfall," he said. He said poor maintenance of drains and waterways clogged with rubbish compounded the problem.
ABS-CBN television showed a dramatic video of more than a dozen people perched on roofs of damaged houses being swept away by the suburban Marikina river. They smashed against the pillars of a bridge and were separated from each other in the rampaging river. It was unclear whether they were rescued.
Cruz said seasonal monsoon rains were intensified by tropical storm Ketsana, which packed winds of 85 kph with gusts of up to 100 kph when it hit land early yesterday about 80km north-east of Manila. It was moving westward toward the rice-producing Central Luzon region at 19kph. Stranded residents called radio and television stations for help.