More than 100,000 people sought shelter in five province east and south of the capital in the path of Typhoon Mirinae on the main Luzon Island. One river in Laguna province south of Manila overflowed, flooding most of lakeside Santa Cruz town and sending residents clambering onto roofs to escape rising waters, said Mayor Ariel Magcalas.
"We cannot move, this is no joke," Magcalas said. "The water is high. We need help," he said in a public address via Radio DZBB.
Rescue teams were dispatched to the flooded communities but were having difficulty moving in light trucks, said regional disaster officer Fred Bragas.
"As of now, our efforts are concentrated on rescue and evacuation," he said.
There were no immediate reports of casualties.
In Manila, residents hunkered down in their homes overnight as rains beat down on dark, deserted streets. Mirinae passed south of the sprawling city of 12 million with winds of 93 miles (150 kilometers) per hour and gusts of up to 115 mph (185 kph).
The fourth typhoon to lash in the Philippines in a month, Mirinae was tracking the same route as Tropical Storm Ketsana on Sept. 26 when it dumped the heaviest rains in 40 years in and around Manila - a month's worth in just 12 hours - leaving hundreds dead and thousands stranded in cars, on rooftops and in trees.
Strong winds toppled trees and power poles, slowing traffic on some highways, radio stations reported. Manila electric power distributor Meralco said the winds had forced outages in many areas around the capital and nearby areas.
Commuter train service was disrupted, flights at Manila international airport were canceled and about 8,000 ferry passengers were stranded as the coast guard grounded all vessels.
Unlike Ketsana, the latest typhoon was quick - moving fast at 15 mph (24 kph). It was projected to veer away from the Philippines in the direction of Vietnam by later Saturday.
At least 10,000 villagers left their homes near rivers and close to the Mayon volcano in Albay province, said Jukes Nunez, a provincial disaster official.
Mayon, in the eastern Philippines, is the country's most active volcano and authorities fear that rains might unleash rivers of mud and loose volcanic rock.
In Arenda village, where knee-deep waters still lingered a month after Ketsana hit, Hilaria Abiam was getting ready to leave at a moment's notice from her house along the shore of Laguna Lake, southeast of Manila.
"If the floodwater threatens to rise again, then I will surely evacuate because I am really frightened," she said.
Another resident, Loida Vicente, prepared a boat at her home. "I have a lot of children and if the water rises suddenly, then we will use that to evacuate," she said.
The government's disaster agency told people to prepare 72-hour survival kits, including food items like rice plus a radio set, flashlights and batteries, clothing and first aid supplies.
Ahead of the typhoon, millions of Filipinos boarded buses heading to home provinces for this weekend's All Saints Day, when people visit cemeteries to pay respects to dead relatives in this devoutly Roman Catholic nation.
Defense Secretary Gilbert Teodoro expressed fear that floods and traffic congestion may trap visitors at graveyards, where people traditionally spend a day or even a night, but few heeded his call to scrap their commemorations.
The northern Philippines is still struggling to recover from back-to-back storms that killed 929.
In some provinces, floodwaters raged through cemeteries, breaking up tombs and sweeping away caskets and bodies.
About 122,000 people remain in government-run evacuation centers, and many communities in Manila suburbs are still under water, with residents moving around on makeshift rafts and foot bridges.
Associated Press writers Hrvoje Hranjski and Teresa Cerojano contributed to this report.