At least eight other people have been reported missing and military and volunteer rescue teams were dispatched to the rice-farming province of Nueva Ecija where rivers burst their banks and flooded several villages, authorities said.
"People are asking for help because the floodwaters are rising. The rescuers cannot penetrate the area as of now," Nigel Lontoc, the assistant civil defence chief for the region, told AFP.
Television footage showed raging brown rivers swallowing up homes and carrying off large debris including tree trunks.
ABS-CBN network showed a photograph of blue-clad police holding onto a rope and wading in chest-deep floodwaters to rescue trapped residents.
More than 23,000 have been displaced after Typhoon Koppu roared into northern Philippines.
The government said more than 23,000 people had already been evacuated from the path of Koppu, which also disrupted ferry services and aviation.
Koppu made landfall before dawn on the remote fishing town of Casiguran, whipping the coast with gusts of up to 210 kilometres (130 miles) an hour for nearly seven hours before moving inland.
"Koppu tore off roofs of homes made of light materials. Rivers overflowed, and the roads to the area are blocked by downed power pylons and trees," Lontoc said.
It later crossed over the Pantabangan Dam in the southern foothills of the Cordillera, the country's largest mountain range, with gusts of 185 kilometres an hour.
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Filipinos carry their belongings at Manila Bay in Manila, Philippines, 18 October 2015. - EPA/Mark R. Cristino
A big tree toppled and crushed a house in Manila, killing a 14-year-old boy and injuring four other people, Alexander Pama, head of the National Disaster Risk Reduction Council, told reporters in Manila.
Officials said more people are expected to flee as the now weakened storm makes its way to the northern tip of Luzon, the Asian country's largest island and home to about half its national population of 100 million people.
Aurelio Umali, governor of Nueva Ecija province that includes Pantabangan told ABS-CBN said rescuers saw two human bodies floating in one of the flooded villages.
However Lontoc said the two bodies have not been recovered.
Lontoc said three people in the coastal resort town of Baler, near Casiguran, are missing after a large wave struck their house, and three fishermen are also missing on Manila Bay.
'Flood warning'
The authorities warned heavy rains could still trigger flash floods and landslides in the Cordillera, known for its spectacular rice terraces carved on the slopes of towering mountains.
"I must emphasise that this is just the start. People must remain alert while we try to pick up the pieces in areas already hit," Pama said, as he urged local officials to evacuate Cordillera villages deemed most at risk.
Lontoc said the rain-soaked mountains also posed a threat to the heavily populated central Luzon region just north of Manila in the coming days.
With dams filling up and forced to let off water, he said huge volumes of runoff are streaming into the Pampanga river, which spills onto the region.
The weather service said Koppu would weaken further into a tropical storm by Tuesday, but continue to dump rain before heading for Taiwan on Wednesday.
It caused widespread power and communications disruptions across Luzon, with many roads and bridges also blocked by landslides, floods or fallen trees and power pylons.
Thousands were stranded as ferry services were suspended amid rough seas while 44 commercial flights were cancelled, including four international flights, Pama said.
The Philippines suffers an average of 20 storms each year.
Super Typhoon Haiyan, the strongest and deadliest on record, destroyed entire towns in the central islands in November 2013, leaving more than 7,350 people dead or missing.
