At least seven people were killed as Typhoon Nesat smashed the Philippines, authorities said Tuesday, with the capital of Manila enduring waist-deep floods, blackouts and dramatic storm surges.

The Philippines are hit by about 20 major storms annually, many of them deadly, but the government said Nesat was one of the largest to the country had faced this year, with its rain and wind path twice as big as average.

"This storm is very intense, the rain is strong and winds are powerful... we are hearing of rivers about to burst their banks, and there are evacuations on going in different areas," civil defence chief Benito Ramos told AFP.

"We do not have exact figures on how big the damage is... as the storm is still battering us."

However the civil defence office confirmed at least seven people had died, four of them in Manila when a building collapsed.

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 bay just rose over the seawall. We are advising people not to leave their homes and stay safe. Those living near the bay should be vigilant," Philippine National Red Cross secretary general Gwen Pang told AFP.

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.

"We've heard of Manila Hospital being flooded, but we're struggling to reach the area even though we've coordinated with them already to help in an evacuation plan," Pang said.

The five-star Sofitel Philippine Plaze Hotel, located on the bay, was also evacuated, rescue workers said.

About 5,000 people living inland along the Marikina River were ordered to leave their homes because the waterway was threatening to overflow its banks, presidential spokesman Edwin Lacierda told reporters.

The presidential palace announced the suspension of all school classes and work for government agencies in Manila and other affected areas, while dozens of domestic flights in and out of the capital were cancelled.

The Philippine Stock Exchange suspended trading, while Manila's main overhead railway system ground to a halt due to power failures that affected more than third of the city.

Nesat hit the northeastern side of Luzon before dawn, bringing maximum sustained winds of up to 140 kilometres (87 miles) an hour and gusts clocking in at 170 kilometres an hour.

It was expected to slowly travel across the mountainous, remote farming areas of northern Luzon throughout Tuesday and Wednesday, continuing to dump heavy rains across the whole island that is home to about 48 million people.

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.

The first fatality occurred on Monday night when a swollen river in the east swept away a baby boy.

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.