Five people were also killed in the storm, two of them electrocuted while wading through flood waters, an emergency official said.
Manila and the northern provinces were worst hit, with residents being rescued from the roofs of flooded homes.
Fung-Wong is now heading north, and is expected to hit Taiwan on September 21.
Some 50,000 troops have been placed on standby on the island for potential rescue and relief operations.
The flood waters began to subside in parts of the Philippines on Saturday, allowing displaced residents to return home and begin clearing up.
Fung-Wong had struck the archipelago with winds of 59mph and gusts of 70kph, gathering strength as it moved north. Three weeks’ worth of rain is reported to have fallen overnight in parts of the country.
Roofs were blown away, trees toppled and highways flooded across the island of Luzon, seat of the capital, Manila.
Local media reported a river burst its banks in an eastern part of Manila on September 19, prompting the evacuation of more than 20,000 people. Other residents, however, chose to stay put.
Fung-Wong also lashed Cebu City in central Philippines, leaving parts of it 6ft underwater.
Tropical storms frequently strike the Philippines: Fung-Wong is the second in two weeks.
y001Vej4UOQAt least five people, including a four-month-old baby, have been killed after dozens of tornadoes…
Harvey Weinstein has been hospitalized just days after his 2020 rape conviction in New York…
Hamas has published a video showing the first proof of life of US and Israeli…
Prosecutors and Donald Trump’s attorneys delivered opening statements and the first witness was called on…
The House of Representatives has finally approved $61 billion in new US military aid for…
The real estate market in the United States has always been a gauge for economic…