The typhoon made seven landfalls before heading to the South China Sea.
As of Thursday morning, the Philippine weather agency, PAGASA, said that Phanfone was reported 155 kilometres west of the province of Palawan, with maximum winds of up to 130 kilometres per hour and gustiness of up to 160 kilometres per hour.
The typhoon brought a wet and miserable season to many who were holidaying in the island nation and stranded thousands as dozens of flights were cancelled.
Local authorities had started evacuating people in risky areas to safer government facilities before the typhoon made landfall on Tuesday afternoon in Eastern Samar province.
The storm left a trail of destruction as it swept across the central Philippines and areas off the southern tip of the main Luzon island. Huge flooding was reported in many affected areas.
The Philippines is one of the most disaster-prone countries in the world mainly due to its location in the Pacific Ring of Fire and Pacific typhoon belt. Landslides and flash floods are common during the rainy season, especially when a typhoon hits the island country.