The quake sent people rushing out of homes and buildings, including hospitals, as aftershocks continued. At least five died in a stampede in Cebu, said Neil Sanchez, provincial disaster management officer.
Offices and schools were closed for the Muslim festival of Eid al-Adha, which may have saved lives.
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Four people were killed in Bohol and 15 died in Cebu province, a more urban and densely populated region across the strait from the earthquake's epicenter, said Civil defense spokesman Maj. Reynaldo Balido.
Another person died on Siquijor Island, southwest of Bohol. A total of 33 were injured.
In Cebu, a boat ride from Bohol, five were killed when a fishing port collapsed. Two more people died and 19 were injured when the roof of a market in Mandaue in Cebu province fell on them. Elsewhere in the city, a woman died after being hit on the head when the quake toppled a building.
Photos from Cebu broadcast on TV stations showed a fallen concrete 2-story building, and reports said an 8-month-old baby and a second person were pulled out alive.
"It's fortunate that many offices and schools are closed due to the holiday," said Jade Ponce, the Cebu mayor's assistant.
He said patients at the city's hospitals were evacuated to basketball courts and other open spaces "but we'll move them back as soon as the buildings are declared safe."
Historic churches suffered the most damage, including the country's oldest, the Basilica of the Holy Child in Cebu, which lost its bell tower.
Cebu province, about 570 kilometers south of Manila, has a population of more than 2.6 million people. Nearby Bohol has 1.2 million people and is popular among foreigners because of its beach and island resorts and the Chocolate Hills.
The quake also was deeper below the surface than the 6.9- magnitude temblor last year in waters near Negros Island, also in the central Philippines, that killed nearly 100 people.
Regional military commander Lt. Gen. Roy Deveraturda said that he recalled soldiers from the holiday furlough to respond to the quake.
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