The third typhoon to hit the storm-battered Philippines in as many weeks caused major flooding in Manila on Thursday, trapping some people on rooftops and claiming at least one life in another part of the country.

Typhoon Vamco packed winds of up to 155 kilometres (96 miles) per hour as it swept across Luzon after making landfall overnight, with authorities warning of landslides and potentially deadly storm surges along the coast.

Heavy rain effectively shut down Manila, the sprawling capital of 12 million people, and surrounding areas.

"A lot of places are submerged. Many people are crying for help," said Rouel Santos, 53, a retired disaster officer in Rizal province, next to Manila.

Santos said the flooding caused by Vamco brought back memories of the devastating Typhoon Ketsana, known in the Philippines as Tropical Storm Ondoy, that hit in 2009 and claimed hundreds of lives.

At least one person died and three others were missing in Camarines Norte province, the country's Office of Civil Defense said late Wednesday.

The weather service warned of life-threatening storm surges several metres (feet) high along parts of the coast, including in Manila, that could inundate low-lying areas.

The Bicol region, which Vamco grazed before making landfall, was hit by powerful winds and heavy rain on Wednesday as the eye of the typhoon neared the disaster-prone archipelago. 

The area, which includes Catanduanes Island, is still reeling from deadly typhoons Molave and Goni, which killed dozens of people and destroyed tens of thousands of homes.

Swathes of Bicol remain without power and with only limited or no telecommunication services after Goni -- the most powerful typhoon so far this year -- toppled power lines, flattened houses and flooded roads.

The Philippines is hit by an average of 20 storms and typhoons every year, which typically wipe out harvests, homes and infrastructure in already impoverished areas.