Slow-moving Typhoon Hagupit has weakened as it churns across the central Philippines islands, easing fears of widespread mass destruction, but officials warn the storm could still bring severe flooding to the low-lying capital Manila.

Since slamming into the island of Samar on Friday night, Hagupit has killed at least three people while flattening houses, toppling  trees and knocking out power lines.

But the storm with a 600-kilometre front has not wreaked destruction of the same scale as Super Typhoon Haiyan that hit the country last year, leaving 7300 dead and displacing 4.1 million others.

Residents walk past high waves brought about by strong winds as it pound the seawall, hours before Typhoon Hagupit passes near the city of Legazpi. Photo: AFP

One million people fled to the safety of 1500 schools, civic centres, churches and other makeshift evacuation centres ahead Hagupit, the strongest storm to hit the Philippines this year.

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Weather forecasters say that as Hagupit grinds west-northwest across the Philippines, the danger will gradually transition from wind damage and storm surges to heavy rainfall.

Its centre is expected to move agonisingly slow in the general direction of Metro Manila, taking 48 to 72 hours to move from the eastern Philippines to the capital.

Typhoon Hagupit hits the Philippines. Photo: AFP

Forecasters say that while Hagupit's winds will continue to weaken as it approaches Manila, it will remain strong enough to bring down trees and cause power outages.

Visiting the Philippines, Greenpeace global chief Kumi Naidoo blamed climate change for increasingly violent storms hitting the country.

"Nature does not discriminate. We actually have to wake up and smell the coffee. We need to understand we are running out of time," he said, in a warning to negotiators meeting in Lima, Peru, to hammer out the broad outlines of a new world pact on global warning.

Mr Naidoo said the typhoon passing over the Philippines was an example of the massive damage poorer countries would experience if climate change worsens.

He said the storms hitting the South-East Asia archipelago were getting stronger and stronger, showing the urgency for world governments to act.

The Philippines endures an average of 20 typhoons a year.

Millions of people remain in the path of Hagupit, which is called Ruby locally.

After making landfall with wind gusts up to 220 kilometres per hour the storm's punch weakened on Sunday and early Monday to gusts of 170 kilometres per hour.

In Manila, a city of 12 million people, authorities have closed schools and tens of thousands of slum dwellers have been evacuated from coastal shanty homes vulnerable to heavy flooding.

The storm is expected to dump intense rain across the country before exiting into the South China Sea on Tuesday.

-With agencies