The casualties, majority inflicted late on Friday, were all on the main southern island of Mindanao as rescuers pulled dozens of bodies from a swollen river, police said.
Rescuers also retrieved 36 bodies from Salog River in Zamboanga del Sur on Saturday.
The Philippines is pummelled by 20 major storms each year on average, many of them deadly.
A policeman carries a young girl as he wades through a flooded street in Cagayan City on December 22, 2017, after the Cagayan River swelled caused by heavy rains brought by Tropical Storm Tembin.
A state of calamity had also been declared in Lanao del Norte and Lanao del Sur.
"Initial information reports (deaths) due to flash flood".
As severe Tropical Storm Vinta made a landfall in Davao Oriental early Friday morning, hundreds of families residing in flood-prone areas here left their homes and sought shelter in the city's evacuation centers.
Lanao del Norte officials reported the highest death toll at 64 with 139 missing followed by Zamboanga del Norte province, where officials reported at least 29 storm deaths with 19 others missing.
Presidential spokesman Harry Roque, in a statement, said it is saddening that the events, especially the onslaught of Vinta happened a few days before Christmas.
It struck the southern section of western Palawan province late Saturday (local time) and is forecast to blow away from the southern Philippines on Sunday toward the South China Sea.
In Lanao del Sur, the death rose to 18 after 10 more fatalities were reported in Piagapo town, where 40 houses were buried by boulders, civil defence officer Saripada Pacasum of Lanao del Sur province said.
Last week, 46 people were killed in the central Philippines when a typhoon hit.