Typhoon Nesat also forced the closing of the Philippine Stock Exchange and the US embassy, and the ground floor of Manila’s main hospital was flooded.
At least seven people have been killed, including several children.
Nesat is expected to continue slowly across the country, before blowing across the South China Sea towards southern China on Thursday.
The typhoon made landfall just before dawn on Tuesday in the eastern Isabela and Aurora provinces on the Pacific coast.
The storm – with a diameter of 650km (400 miles) and wind gusts of up to 170km/h (105mph) – is now making its way across Luzon, the main island.
Many roads have been flooded and flights cancelled, and local media are urging people against non-essential travel.
An adult and three children were crushed to death as a building collapsed in a northern Manila suburb on Tuesday, AFP news agency quoted the Office of Civil Defence as saying.
Two men were said to have died north of the capital in a landslide and weather-induced accident.
There is waist-deep flooding in parts of the capital.
Reporters described huge waves crashing into Manila Bay’s seawall, with water overflowing into Roxas Boulevard and flooding streets and parks around the US embassy, which was evacuated.
The ground floor of Manila hospital was flooded, and staff was forced to move patients to the first floor.
“We’ve heard of Manila Hospital being flooded, but we’re struggling to reach the area even though we’ve co-ordinated with them already to help in an evacuation plan,” Philippine National Red Cross secretary general Gwen Pang told AFP.
It was reported that a five-star hotel was also evacuated.
Thousands of residents living inland along the Marikana river were evacuated as it threatened to overflow.
Government offices, schools and universities were closed.
In Isabela province, four coastal towns under threat from storm surges have been evacuated.
Four fishermen are missing, and more than 50 more have been rescued after their boats capsized in rough seas.
There are fears that the death toll may rise further.
Earlier, about 110,000 people in several towns of the Albay province were ordered to leave their homes and seek shelter elsewhere.
“We can’t manage typhoons, but we can manage their effects,” provincial Governor Joey Salceda was quoted as saying by the Associated Press.
The Philippines suffers frequent typhoons, about 20 a year, but Nesat is thought to be the largest this year.
Typhoon Nesat comes almost exactly two years after Typhoon Ketsana killed more than 400 people.
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