Heavy rains triggered landslides and left parts of the country under water as Typhoon Chanchu headed northwest towards the South China sea.
More than 10,000 people were stranded because air and ferry service was halted.
Windspeeds of up to 120km per hour were recorded near the centre of the storm.
Most of those killed were from a boat that capsized off Masbate island in the south of the Luzon region, the Coast Guard said.
At least 21 people on the vessel, named the Mae Ann 5, were killed and 18 were rescued, Coast Guard spokesman Joseph Coyme told reporters in Manila.
A fisherman drowned while four others were rescued when their boat sank in rough seas off the coast of Negros Occidental province in the central Philippines, Coyme said.
In Batangas province, near Manila, a 36-year-old woman was killed when a fence swept by floods crashed into her hut, officials told local radio.
Passengers wait at a Manila bus
station for service to resume
The National Disaster Coordinating Council said a boy was killed in Laguna province after he was pinned by a coconut tree toppled by Typhoon Chanchu.
Eight fishermen were also missing, the council said.
The authorities said 23,000 people in the east and centre of the country had been evacuated.
Floodwaters submerged two central provinces, and several villages on the island of Leyte were cut off after landslides damaged a bridge and a motorway.
Two tugboats located a ferry with 700 passengers aboard that had gone missing in rough seas but was found anchored off a cove near Mindoro island.
A swollen river broke a dike early on Saturday and submerged four villages under waist-deep water – also on Mindoro island.
Villages on Leyte were cut off
The storm ripped tarpaulin billboards off their steel frames along several roads in metropolitan Manila, where winds toppled several trees but caused no major damage.
Chanchu is slowly moving west but will continue to cause bad weather in the Philippines for another day or so.
Weather website www.tropicalstormrisk.com forecasts the typhoon strengthening to a category four storm, with five the maximum, in the next few days as it turns northwest towards Hong Kong.