The death toll included 59 people who drowned in the central province of Iloilo, with another 40 missing, Gov. Neil Tupaz said.
"Almost all the towns are covered by water. It's like an ocean," Tupaz said, adding thousands have been displaced in the province that is home to 1.7 million people.
TV footage showed rescuers holding on to a long rope strewn across raging floodwaters in an Iloilo village to pluck three residents trapped on top of a partly engulfed van. In a nearby village, residents pulled out a body from a muddy field then laid it beside another they found earlier.
Villagers found four bodies, children's slippers and life jackets that washed ashore on Sunday near the stalled MV Princess of Stars. Port captain Nestor Ponteres said the ferry's owner, Sulpicio Lines, had lost radio contact with the ship and the fate of its passengers was unknown.
A rescue ship reached the site after battling huge waves and strong winds but found no other survivors. "They haven't seen anyone. They're scouring the area. They're studying the direction of the waves to determine where survivors may have drifted," coast guard spokesman Lt. Senior Grade Arman Balilo said.
The dead, including a man and a woman who bound themselves together, were believed to have been on the vessel, which initially ran aground a few kilometres off central Sibuyan island on Saturday, then capsized, said Mayor Nanette Tansingco of San Fernando on Sibuyan island.
At least three survivors from the ferry were found in Sibuyan's Mabini village and police were ordered to go there. But all the roads to the village, where many houses were washed away by huge waves, were blocked by toppled trees, Tansingco told DZBB radio.
She appealed for food, medicine and formalin, apparently expecting many deaths in her town. The upturned ferry, its bow jutting out of the water, could be seen from her town, she said.
The typhoon lashed the central Philippines for about four hours on Saturday, setting off landslides and floods, knocking out power and blowing off roofs.
Packing sustained winds of 120 kilometres per hour and gusts of up to 150 kph, the typhoon shifted course on Sunday to the northwest and battered Manila at dawn, dumping heavy rain on the capital.
Rescue vessels aborted an initial attempt on Saturday to get to the 23,824-ton ferry, but efforts resumed in stormy weather on Sunday, coast guard chief Vice Admiral Wilfredo Tamayo said.
"A lot of efforts have been done to send off rescue boats, but we really can't get through the very rough weather," Tamayo told The Associated Press.
Tansingco said the bodies were found in three San Fernando villages, adding residents have also found other objects that apparently came from the ferry.
"Many slippers of children were washed ashore the shoreline and found by villagers," Tansingco told DZBB radio.
The ferry - with 626 passengers and 121 crew members on board - was "dead in the water" after its engine failed around noon on Saturday, Tamayo said.
About two dozen relatives trooped to the Manila office of Sulpicio Lines, some quietly weeping as they waited for news about the fate of their loved ones. "I'm very worried, I need to know what happened to my family," said Felino Farionin, his voice cracking. His wife, son and four in-laws were on the ferry.
In southern Maguindanao province, at least 14 people drowned in flash floods Saturday, including 10 swept away from riverside homes, said provincial administrator Norie Unas. Five others were missing.
A 50-year-old man and his 10-year-old grandson were killed when a landslide buried their hillside shanty in Cotabato city Saturday, Mayor Muslimin Sema said. Authorities recovered the body of a farmer, one of three people reported missing in neighboring Cotabato province.
President Gloria Macapagal Arroyo directed the defense and local government departments to stand by for relief and rescue missions before she left for the United States late on Saturday.
Arroyo later talked to officials in a teleconference aired live on nationwide radio, scolding coast guard officials for allowing the ferry to leave Manila late on Friday despite the bad weather.
