Typhoon Nesat has smashed into the Philippines, leaving at least 16 people dead, with the capital Manila enduring waist-deep floods, blackouts and dramatic storm surges.

The Philippines is hit by about 20 major storms annually, many of them deadly, but the government said Nesat was one of the largest the country had faced this year, packing twice as much rain and wind as an average storm.

"This storm is very intense, the rain is strong and winds are powerful," civil defence chief Benito Ramos said.

"We are hearing of rivers about to burst their banks, and there are evacuations ongoing in different areas. We do not have exact figures on how big the damage is ... as the storm is still battering us."

He later told AFP that at least 16 people were killed as of 7.00 pm (local time) on Tuesday, with the toll likely to rise overnight as more reports from rescuers on the ground were expected to filter in.

He said four of the dead were crushed by a collapsed structure in Manila, while a baby fell into a raging river in an eastern province on Monday.

More than 100 other people were rescued, including fishermen whose boats capsized in rough seas after they ignored warnings not to set sail.

Nesat slammed into the main island of Luzon before dawn on Tuesday, bringing maximum sustained winds of up to 140 kilometres per hour and gusts clocking 170kph.

It later weakened while slicing through Luzon, but dumped heavy rains throughout the day across the whole island that is home to about 48 million people.

Parts of the capital, a sprawling megacity of more than 12 million, endured waist-deep flooding, with some of the worst impacts seen around the historic bayside area.

Huge waves crashed into Manila Bay's seawall, sending water spraying over into the picturesque Roxas Boulevard and closing one of the city's main arteries to traffic.

The ground floor of Manila Hospital, which sits on the boulevard facing the bay, was submerged in knee-deep waters, forcing medical staff to relocate patients to the second floor, radio station DZBB said.

The five-star Sofitel Philippine Plaza Hotel, located on the bay, was also evacuated, while the US embassy was partly submerged, according to rescue workers.

Nearly 2 million households suffered power outages in the capital and surrounding areas, according to the Manila Electric Company, and many people remained without electricity by nightfall.

Amid the chaos, all schools were suspended and government offices were closed, while dozens of domestic flights in and out of the capital were cancelled.

The Philippine Stock Exchange suspended trading, and Manila's main overhead railway system ground to a halt due to power failures.

A controlled release of water from the Angat Dam in Bulacan province just north of Manila on Tuesday flooded around 25 towns, provincial governor Willy Alvarado said, though there were no reports of casualties.

"We will continue evacuating people into the night," he said on state radio.

The state weather bureau said Nesat was expected to blow into the South China Sea by Wednesday, although bad weather would likely persist for most of the week.

The agricultural provinces of Isabela and Aurora in the east of the country, among the Philippines' leading rice-producing areas, were the most heavily affected initially, the state weather bureau said.

Isabela governor Faustino Dy said about 1,400 people had been relocated to 17 evacuation centres from four coastal towns in his province to avoid powerful storm surges.

About 110,000 residents had already been evacuated from several flood-prone towns in Albay, another eastern province, on Monday.

AFP