Millions of people in the Philippine capital are hunkering down as a major storm churns towards the megacity after killing at least 21 people.

However, Hagupit has weakened from a typhoon after moving slowly across the central Philippines, fuelling cautious optimism the disaster-weary nation may avoid another calamity involving hundreds of deaths.

In Metro Manila, a sprawling coastal megalopolis of 12 million people that regularly endures deadly flooding, well-drilled evacuation efforts went into full swing on Monday as forecasters warned of heavy rain from dusk.

"We are on 24-hour alert for floods and storm surges ... it's the flooding that we are worried about," Joseph Estrada, mayor of Manila, the original city of two million within Metro Manila, said.

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Thousands of people, mostly the city's poorest who live in shanties along the coast and riverbanks, crammed into schools and other evacuation centres across Metro Manila.

Schools were suspended, the stock market was closed, many office and government workers were told to stay at home, and dozens of commercial flights were cancelled.

The preparations were part of a massive effort led by President Benigno Aquino to ensure minimum deaths, after 7350 people died when Super Typhoon Haiyan devastated large parts of the central Philippines in November last year.

Millions in communities directly in the path of Hagupit over the weekend were sent to evacuation centres or ordered to remain in their homes.

The storm, the strongest to hit the Philippines this year with wind gusts of 210 km/h when it made landfall, caused massive destruction in remote farming and fishing towns.

Thousands of homes were destroyed, power lines were torn down, landslides choked roads and flood waters up to one storey high flowed through some towns.

Hagupit claimed at least 21 lives, with 18 of them on Samar island where the storm made landfall, Philippine Red Cross secretary-general Gwendolyn Pang said.

Sixteen people died in Borongan, one of the main cities along Samar's east coast that faces the Pacific Ocean and about 50 km south of where Hagupit struck, according to Pang.

She said it was impossible to say whether the death toll would climb, with full damage assessments from some areas yet to come in and the storm still travelling across the country.

Hagupit's sustained winds dropped to 140 kilometres an hour on Sunday, then continued to weaken after leaving the eastern Philippine islands and passing over the Sibuyan Sea southeast of Manila.

Its winds were down to 110 kilometres an hour on Monday and were expected to weaken further as it passed just south of the capital in the evening, according to local weather agency Pagasa.

However, Pagasa said the winds were still capable of doing major damage to homes, and heavy rains were expected within Hagupit's 450-kilometre-wide weather front.