Despite finding only corpses in recent days, navy and coastguard ships and helicopters continued to scour the waters for the 45 still missing from the St Thomas Aquinas ferry, said local coastguard commander Weniel Azcuna.
"We are still hoping to find more survivors but we are realistic and we expect we will find more dead bodies," he said.
The ferry sank quickly after it collided with a cargo ship off the central city of Cebu on Friday night.
A total of 750 passengers and crew out of the 870 on board were rescued.
Azcuna said divers were still searching the debris-choked vessel, and declined to set a date for when the operation would end.
The new toll was up by four from Wednesday.
The number of people who died in a ferry sinking in the central Philippines rose to 52 on Monday as divers retrieved more bodies from the sunken wreck, the coast guard said.
Sixty-eight people are still missing after the ferry, MV St Thomas Aquinas, sunk in a collision with a cargo ship off the coast of Cebu province, 580 kilometres south of Manila, on Friday.
Authorities fear most of the missing were trapped in the 11,405-ton ferry, which was lying some 45 metres below the sea.
The coast guard said divers recovered 11 bodies from the St Thomas on Monday morning, but rough seas were slowing down the operations.
The ferry was carrying 870 people when it collided with the cargo ship MV Sulpicio Express 7 as they passed a narrow channel off the port of Talisay City.
The cargo ship's 38 crew members were unharmed, while 750 people on the St Thomas have been rescued, the coast guard said.
Philippine authorities said Sunday they were unable to stop fuel leaking from a ferry that sank, as oil spread to coastal villages, fishing grounds and mangroves more than five kilometres (three miles) away.
The St Thomas Aquinas ferry sank on Friday night after colliding with a cargo ship just outside the port in Cebu, the Philippines' second biggest city, leaving at least 34 people dead.
Authorities were focused Sunday on trying to find 85 people missing and believed inside the ferry, about 30 metres (100 feet) under water, but the leaking oil added a new front to the disaster response.
"You can see it coming out of the sunken vessel. It is bunker fuel and it is black," Cebu coastguard commander Weniel Azcuna said.
"It has affected a lot of shorelines here in Cebu and (the neighbouring island of) Mactan."
He said there was about 120,000 litres (31,700 gallons) of bunker fuel, and divers had been unable to reach the source of the leak.
Among the areas affected were Lapu-Lapu City and Cordova town in Mactan island, and Talisay city in Cebu, which all host popular beach resorts.
Cordova also has protected mangrove areas while Talisay has a thriving fishing industry.
At Cordova, roots of mangroves were coated in black oil at low tide, according to an AFP reporter who visited the area, which is more than five kilometres from where the ferry sank.
Herons and egrets waded amid shallow water that had a rainbow sheen of oil.
Azcuna said that because the hole could not be plugged, the coastguard and a company contracted by the ferry operator were spraying a chemical dispersant to try and break it up.
He could not say how much of the fuel had leaked out already.
An official with the ferry operator told ABS-CBN television the company intended to bring in foreign experts who could safely pump out the remaining fuel.
Rescuers on Sunday prepared to dive in rough seas in the central Philippines to search for more than 100 people missing and feared trapped in a sunken ferry, the coast guard said.
Bad weather brought on by a tropical depression has been hampering the search operations in Cebu province, 580 kilometres south of Manila, where the MV St Thomas Aquinas sank Friday after colliding with a cargo ship.
"Divers need to familiarise themselves with the floor plan of the sunken ferry to know the pathways and exits," he said. "They need to plan how to enter the ship without putting themselves in danger."
The death toll from a ferry sinking in the central Philippines rises to 35 as rescuers search for more than 200 still missing Saturday, the military said.
Emergency workers have rescued 630 people from the waters off Talisay City in Cebu province, 580 kilometres south of Manila, where the MV St Thomas Aquinas sank on Friday evening after colliding with a cargo ship.
Lieutenant Jim Alagao, spokesman for the military's central command, said 216 people were still missing.
The coast guard said 870 people were on board the ferry but the ship's owner said only 841 people were on its initial manifest. The vessel has an authorized capacity of 1,010.
At least two people were killed Friday when a ferry carrying hundreds of passengers sank in central Philippine waters after colliding with a cargo vessel, the police and coast guard said.
The MV Saint Thomas of Aquinas was believed to be carrying 692 passengers when it collided with the cargo ship MV Sulpicio Express 7 off the coast of Talisay City in Cebu province, 580 kilometres south of Manila.
"Two unidentified casualties were retrieved while survivors were brought to hospitals," said Chief Superintendent Generoso Cerbo Jr, a regional police director.
"Rescue operations are being hampered by zero visibility," he added. "It's very dark in the area, but more emergency teams have been dispatched."
Authorities said they were still verifying the number of survivors.
Many passengers of the Saint Thomas of Aquinas were forced to jump into the sea after the vessel was badly damaged by the collision, said coast guard vice commandant Rear Admiral Luis Tuason Jr.
The passenger ferry was travelling to Manila via Cebu City from the southern province of Agusan del Norte when the accident occurred, Tuason said.
The Sulpicio Express was travelling from Cebu City to the southern city of Davao, he added.
Sea travel is a key mode of transportation in the Philippines, an archipelago of more than 7,000 islands. But accidents are common due to poor safety standards and overloading.
The country was the site of the world's worst peacetime maritime disaster when a ferry collided with an oil tanker days before Christmas in 1987, killing more than 4,300 people.
The Philippines coastguard launched a rescue mission Friday night after a ferry carrying almost 700 people collided with a cargo ship off the central city of Cebu, officials said.
The Thomas Aquinas ferry, carrying 692 people, collided with the freighter Sulpicio Express 7, coastguard spokesman Commander Armando Balilo said.
He added one of the vessels was listing but could not identify which one.
Voice of Russia, DPA, AFP, NPA, Reuters