Tropical depression Merbok crashed into the east coast of the main island of Luzon on Tuesday, dumping heavy rain that unleashed floods which swept away at least 13 people in the towns of Dingalan and San Luis, the authorities said.
Some 2,000 people fled their homes.
Two air force helicopters were scrambled to the area to airlift three children who were injured by fallen logs.
The civil defense office said military trucks and rubber boats were also dispatched to the area to help with the rescue.
Several roads in Aurora province, including in Dingalan and San Luis, were blocked by floods or landslides. Damage estimates were not yet available.
Dingalan was the hardest hit, suffering most of the fatalities and with about 200 houses damaged, the civil defense office said.
The air force said the town had been isolated by floods and was running out of food and supplies.
The latest destruction came after tropical storm Muifa cut across the country, leaving many drowned or missing at sea after capsizing and sinking at least eight fishing and cargo boats south of Luzon.
Another 89 people were injured. Some of the over 200,000 displaced people have since started returning home.
Over 9,700 houses were destroyed by the first storm while initial damage estimates to agriculture, infrastructure and private business hit 147.5 million pesos (2.64 million dollars), the office added.
After lashing the Bicol peninsula early last week, Muifa went for a second pass at the weekend before plowing through the islands of Marinduque, Mindoro and Coron on its way to the South China Sea.