More than 300,000 people fled their homes and beachfront resorts as Typhoon Rai ravaged the southern and central regions of the archipelago.
The storm knocked out communications and electricity in many areas, ripped off roofs, damaged hospitals, toppled concrete power poles and flooded villages.
Arthur Yap, governor of the popular tourist destination Bohol, said on his official Facebook page that mayors on the devastated island had so far reported 63 deaths in their towns.
Ten people also died on the Dinagat Islands, provincial information officer Jeffrey Crisostomo told AFP.
That took the overall number of reported deaths to 99, according to the latest official figures.
But the toll was likely to rise as disaster agencies assessed the full extent of the death and destruction from the storm across the vast archipelago.
Rai smashed into the country Thursday as a super typhoon packing wind speeds of 195 kilometres per hour.
Thousands of military, police, coast guard and fire personnel are being deployed to assist in search and rescue efforts in the worst-affected areas.
Coast guard and naval vessels carrying food, water and medical supplies are being dispatched, while heavy machinery -- like backhoes and front-end loaders -- are being sent to help clear roads blocked by fallen power poles and trees.
"It's going to be a long, tough road for people to rebuild and get their lives back on track," said Alberto Bocanegra, head of the International Federation of Red Cross and Red Crescent Societies in the Philippines.
The organisation appealed for 20 million Swiss francs ($21.6 million) to fund urgent relief and recovery efforts.
An aerial survey of damage to parts of Bohol -- known for its beaches, rolling "Chocolate Hills", and tiny tarsier primates -- showed "our people have suffered greatly", Yap said.
There has also been widespread destruction on Siargao, Dinagat and Mindanao islands, which bore the brunt of Rai when it slammed into the Philippines.
Aerial photos shared by the military showed severe damage in the Siargao town of General Luna, where many surfers and holidaymakers had flocked ahead of Christmas, with buildings stripped of roofs and debris littering the ground.
Tourists were being evacuated from the island on Sunday by plane and boat.
Dinagat Governor Arlene Bag-ao has said the damage to the island's landscape was "reminiscent if not worse" than that caused by Super Typhoon Haiyan in 2013.
Haiyan, called Yolanda in the Philippines, was the deadliest cyclone on record in the country, leaving more than 7,300 people dead or missing.
"I saw how Typhoon Odette tore the provincial capitol apart, piece by piece," Dinagat PIO Crisostomo told radio station DZBB, using the local name for Rai.
"Big tables as heavy as a man went flying during the onslaught of the storm," he said.
In Surigao City, on the northern tip of Mindanao, shattered glass from smashed windows, roofing, power lines and other debris were scattered in the streets.
Tricycle driver Rey Jamile, 57, braved flooded streets and "flying" sheets of corrugated iron roofing to get his family to safety at a school evacuation centre.
"The wind was very strong," he told AFP, adding now the storm was over he was struggling to find water and food.
Rai's wind speeds eased to 150 kph as it barrelled across the country, dumping torrential rain, uprooting trees and destroying wooden structures.
It emerged over the South China Sea on Saturday and headed towards Vietnam.
Rai hit the Philippines late in the typhoon season -- most cyclones typically develop between July and October.
Scientists have long warned that typhoons are becoming more powerful and strengthening more rapidly as the world becomes warmer because of human-driven climate change.
The Philippines -- ranked among the globe's most vulnerable nations to the impacts of climate change -- is hit by an average of 20 storms and typhoons every year, which typically wipe out harvests, homes and infrastructure in already impoverished areas.
