At least 21 people were reported dead, many of them drowned as flood waters rose in Borongan, the main town in Eastern Samar, where typhoon Hagupit made first landfall, the Philippine National Red Cross said this morning.
The Philippines had evacuated more than a million people as the powerful typhoon approached the country from the Pacific.
They feared a repeat of last year, when Category 5 "super typhoon" Haiyan tore through the central Philippines leaving more than 7,000 dead or missing.
"We have confirmed reports that 21 people died in Eastern Samar, 16 of them in Borongan," said Gwendolyn Pang, secretary-general of the Philippine National Red Cross this morning.
The National Disaster Risk Reduction and Management Council in Manila confirmed only two dead and three injured.
Two others were reported killed outside Samar, the third largest island in the Philippines, since Hagupit hit on Saturday night.
Hundreds of thousands of Filipinos have returned to their homes.
More than a million people took shelter in evacuation centres across the central belt of the archipelago over the weekend to escape the fury of the Category 3 storm.
Authorities took no chances after last year's storm and evacuated whole towns and villages in coastal and landslide prone areas.
"We're happy that we've learned our lessons from our past experiences. This is a good sign," said Gwendolyn Pang, secretary general of the Philippine Red Cross.
Hagupit roared in from the Pacific on Saturday night, moving across Samar island and on to the smaller island of Masbate.
Its effects were felt across the central Philippines, including Leyte island and the south of the main island Luzon.
"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."
Despite the relief, 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.
Delia Monleon, mayor of Jipapad, a town of 7,000 people in Eastern Samar province, said flood waters were still preventing people from getting to their homes.
"Our problem is power, food is a problem because boats cannot leave," said Ms Monleon.
"It was flooded yesterday so we can't leave to look for food," she said.
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.
In Manila, financial markets, schools and some public officers were closed. People in low-lying areas and near waterways were moved to shelters.
Hagupit was downgraded from a typhoon to a tropical storm this morning, with winds of up to 105km/h and gusts of up to 135km/h.
Aid agency Oxfam has said that it has deployed assessment teams to survey the immediate needs of evacuees "to ensure those who have lost their homes don't lose their health as well."
