Typhoon Koppu made landfall near the town of Casiguran on the main island of Luzon on Sunday morning, bringing winds of close to 200km/h (124mph) and cutting power to vast areas.
A teenager was killed by a fallen tree in Manila which also injured four others. A concrete wall also collapsed in the town of Subic, northwest of Manila, killing a 62-year-old woman, officials said.
By dawn on Monday, wind speeds were down to 150 km/h (93 mph) in the northern town of Santiago, according to the state weather service.
But floodwaters are preventing even military vehicles reaching many of the worst-hit villages, and rescuers report a shortage of boats.
"We haven't reached many areas. About 60% to 70% of our town is flooded, some as deep as three metres," said Henry Velarde, vice mayor of Jaen, a town in Nueva Ecija province.
"There are about 20,000 residents in isolated areas that need food and water.