Evacuated children receive free chocolate rice porridge as they seek shelter at an evacuation centre. Photo: Bullit Marquez/AP

MANILA - The death toll from Typhoon Hagupit rose to 21 on Monday, the Philippine Red Cross said, after the storm tore through the country's central islands flattening homes and toppling trees and power lines.

The capital Manila shut down as Hagupit, now downgraded to a tropical storm, took aim at the tip of the main island Luzon, just south of the city of 12 million people.

"We have confirmed reports that 21 people died in Eastern Samar, 16 of them in Borongan," said Gwendolyn Pang, secretary-general of the Philippine Red Cross. Most of those killed were drowned in floodwaters, she said.

Residents living along coastal areas in Manila take shelter in an evacuation centre. Photo: Bullit Marquez/AP

But despite the jump in the number of reported dead, there was relief that Hagupit had not brought destruction on the scale of super typhoon Haiyan, which last year killed thousands of people in the same areas of the central Philippines.

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Hagupit roared in from the Pacific as a Category 3 typhoon on Saturday night, churning across Samar island and on to the smaller island of Masbate. Its effects were felt across the central Philippines, including Leyte island and southern Luzon.

Learning lessons from Haiyan, which left more than 7,000 dead or missing, the authorities had launched a massive evacuation operation ahead of the storm, emptying whole towns and villages in coastal and landslide prone areas.

A Filipino man carries a dirty plastic sheet from his house after strong waves from Typhoon Hagupit battered a coastal village in Legazpi, Albay province. Photo: Aaron Favila/AP

"We saw that with preparation and being alert we prevented tragedy and harm, we took our countrymen away from harm," Interior Secretary Manuel Roxas told a televised government disaster meeting in Samar. "It is sad to hear news of deaths, but this is very low, way below what the potential was."

The Philippines weather bureau said Hagupit had weakened after making three landfalls, but was still packing winds of 105km/h, with gusts of up to 135km/h.

It was on course to hit Batangas province, around 90km south of Manila, on Monday evening, and would later cross Manila Bay about 50km west of the city.

Residents clean their homes after strong waves from Typhoon Hagupit battered a coastal village in Legazpi, Albay province. Photo: Aaron Favila/AP

Financial markets, schools and some public offices in the capital were closed and people in low-lying areas and near waterways were moved to shelters. Soldiers and emergency workers were put on standby to respond to any contingency.

Clean-up operation

Despite the relief that Hagupit had not been as devastating as was feared, a major operation remained to clear debris and get supplies to people left homeless or without power after the typhoon flattened houses and tore down power lines.

A resident wades in floodwaters bought by Typhoon Hagupit in Camarines Sur province, eastern Philippines, on Monday. Photo: Aaron Favila/AP

Delia Monleon, mayor of Jipapad, a town of 7,000 people in Eastern Samar province, said floodwaters were still preventing people from getting to their homes.

"Our problem is power, food is a problem because boats cannot leave," said Monleon. "It was flooded yesterday so we can't leave to look for food," she said.

Proceso Alcala, the farm minister, said initial reports put crop and farm infrastructure damage at 1 billion pesos ($AU27 million). Rice crops were most affected, with little damage to corn.

Alcala said the state grains agency was considering importing an additional 600,000 tonnes of rice to boost buffer stocks after 48,000 tonnes of unmilled rice was damaged.

Mayor Emiliana Villacarillo of Dolores, in Eastern Samar, the area where Hagupit first made landfall, said almost 100 percent of ricelands in the town were submerged by floodwaters.

"Our farmers will have to go back to square one and plant again. We will need new seedlings," she said.

Armed forces chief of staff General Gregorio Catapang told a news conference two C-130 planes loaded with supplies, including food and water, flew on Monday to Borongan, Eastern Samar, after soldiers had cleared three airports, including Tacloban City.

More than 48,000 residents of Tacloban had fled to shelters, but damage to the city that was devastated by Haiyan in November last year was relatively minor.

"A lot of them have begun to go home. In Tacloban this morning, the sun is shining, people just started going back," said Orla Fagan, spokeswoman and Asia-Pacific advocacy officer at the UN Office for the Coordination of Humanitarian Affairs.

Reuters