The number of deaths, previously at 45, rose as more bodies of missing people turned up, with one man drowning early Monday, said civil defence chief Benito Ramos.

Six people remain missing, including children who went swimming despite the bad weather that began last week as Typhoon Saola approached the country, he added.

Although the Philippines escaped a direct hit, it worsened monsoon rains which continued even after Saola moved north, away from the Philippines.

"They have been evacuating more people since this morning. The waters are still rising because it just keeps raining," Ramos told AFP.

La Mesa Dam, the main reservoir of Metro Manila, which has a population of 15 million, began to overflow Monday, forcing the evacuation of over 1,000 residents living beside nearby waterways, the Metro Manila flood control office said.

However, more people still remain in these areas, many of them squatters who built shanties on riverbanks, said Edna Conda, duty officer at the National Disaster Risk Reduction and Management Council.

"Often they don't want to leave. They say they are used to floods but we don't want to take chances," she said.

In the residential suburb of Quezon City, some areas reported floodwaters reaching the second floor of buildings, forcing various government agencies to rush rubber boats to the area, Conda said.

Other parts of the capital suffered knee- to waist-deep floods snarling traffic for hours, authorities said.

Even before the dam overflowed the government had more than 9,000 people huddled in makeshift evacuation centres, such as schools and basketball courts.