Bohol police chief Dennis Agustin said 77 of the deaths came from the province. At least 15 others died in nearby Cebu province and another on Siquijor Island.
The quake struck at 8:12 a.m. and was centered about 33 kilometers (20 miles) below Carmen city, where many small buildings collapsed.
Many roads and bridges were reported damaged, making rescue operations difficult. But historic churches dating from the Spanish colonial period suffered the most. Among them was the country's oldest, the 16th-century Basilica of the Holy Child in Cebu, which lost its bell tower.
Nearly half of a 17th-century limestone church in Loboc town, southwest of Carmen, was reduced to rubble.
The highest number of dead -- 18 -- were in the municipality of Loon, 42 kilometers (26 miles) west of Carmen, where an unknown number of patients were trapped inside the Congressman Castillo Memorial Hospital, which partially collapsed. Rescuers were working to reach them, said civil defense spokesman Maj. Reynaldo Balido.
As night fell, the entire province was in the dark after the quake cut power supplies. Windy weather and rain also forced back a military rescue helicopter.
Authorities were setting up tents for those displaced by the quake, while others who lost their homes moved in with their relatives, Bohol Gov. Edgardo Chatto said.
Extensive damage also hit densely populated Cebu city, across a narrow strait from Bohol, causing deaths when a building in the port and the roof of a market area collapsed.
The quake set off two stampedes in nearby cities. When it struck, people gathered in a gym in Cebu rushed outside in a panic, crushing five people to death and injuring eight others, said Neil Sanchez, provincial disaster management officer.
"We ran out of the building, and outside, we hugged trees because the tremors were so strong," said Vilma Yorong, a provincial government employee in Bohol.
"When the shaking stopped, I ran to the street and there I saw several injured people. Some were saying their church has collapsed," she told The Associated Press by phone.
As fear set in, Yorong and the others ran up a mountain, afraid a tsunami would follow the quake. "Minutes after the earthquake, people were pushing each other to go up the hill," she said.
But the quake was centered inland and did not cause a tsunami.
Offices and schools were closed for a national holiday -- the Muslim festival of Eid al-Adha -- which may have saved lives.
The earthquake also was deeper below the surface than a 6.9-magnitude temblor last year in waters near Negros Island, also in the central Philippines, that killed nearly 100 people.
Aledel Cuizon said the quake that caught her in her bedroom sounded like "a huge truck that was approaching and the rumbling sound grew louder as it got closer."
She and her neighbors ran outside, where she saw concrete electric poles "swaying like coconut trees." It lasted 15-20 seconds, she said.
Cebu city's hospitals quickly moved patients into the streets, basketball courts and parks.
Cebu province, about 570 kilometers (350 miles) south of Manila, has a population of more than 2.6 million people. Cebu is the second largest city after Manila. Nearby Bohol has 1.2 million people and is popular among foreigners because of its beach and island resorts and famed Chocolate Hills.
President Benigno Aquino III said he would travel to Bohol and Cebu on Wednesday.
Regional military commander Lt. Gen. Roy Deveraturda said he recalled soldiers from holiday furlough to respond to the quake. He said it damaged the pier in Tagbilaran, Bohol's provincial capital, and caused some cracks at Cebu's international airport but that navy ships and air force planes could use alternative ports to help out.
The Philippine archipelago is located in the Pacific "Ring of Fire," where earthquakes and volcanic activity are common. A magnitude-7.7 quake killed nearly 2,000 people on the northern island of Luzon in 1990.
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