The storm, bringing winds of about 120 km per hour (75 mph) and gusts of up to 150 kph, hit Samar and Masbate islands overnight, forcing residents of coastal and low-lying areas to seek higher ground. The Philippines' National Disaster Coordinating Council (NDCC) said two people were confirmed dead, including a 1-year-old girl whose house was pinned by a fallen tree in Capiz province.
Three residents of Roxas City, also in Capiz, were feared dead after they reportedly drowned. The NDCC, however, listed the three as missing, as their bodies had not been found.
Authorities evacuated more than 90,000 residents, most of them in Albay province, where villages were wiped out by Typhoon Durian last week when its winds and rain sent tonnes of mud and water crashing from Mount Mayon, an active volcano, leaving more than 1,000 people feared dead.
The NDCC said nearly 9,000 passengers were also stranded in ports as interisland ferries stopped operations due to rough seas. It said power was knocked out in wide areas in the Visayas region.
The typhoon passed just north of Boracay, a popular tourist destination known for its white sand beaches.
Utor, which brought rain to Manila, is expected to head out to the South China Sea during the next 48 hours on a path that could take it towards northern Vietnam or south China and Hong Kong.
"We expect the typhoon to intensify as it heads over the south China Sea," said Nathaniel Cruz, head of weather forecasting at the Philippines' national weather bureau.
Utor could strengthen to a category 5 "super typhoon" -- with winds of more than 250 kph -- over the sea and is forecast to slam into coastal regions in the northwest of the South China Sea by Friday, according to www.tropicalstormrisk.com.
On Friday, the Philippines hastily postponed an annual summit of 16 Asian leaders until January, citing concerns the typhoon could wreak havoc at the venue on the central island of Cebu.
Presidents and prime ministers from 16 countries were due to start arriving on Cebu and nearby Mactan Island on Saturday for the annual Association of Southeast Asian Nations (ASEAN) meeting and an East Asia summit on Dec. 11-13.
While Philippine officials insisted the surprise move was unrelated to warnings from the US, British and Australian governments that terrorists were planning to bomb the gathering, security officials told Reuters fears of political unrest in Manila had influenced the government's surprise decision.
"We made the right decision, considering the safety of the delegates," Marciano Paynor, Secretary General of the ASEAN Organising Committee, said in Cebu.
Two other typhoons, Cimaron and Chebi, hit the country in late October and early November, causing landslides and flashfloods in some areas and massive damage to property.
Storms regularly hit the Philippines. In one of the worst disasters in recent years, more than 5,000 people died on the central island of Leyte in 1991 in floods triggered by a typhoon.