Rescue efforts were hampered on Friday by the smoky and charred condition of the vessel, which appeared to have drifted closer to shore overnight after attempts to board it were halted because of smoke and heat.
The coastguard said five casualties had been brought ashore after the fire erupted on Wednesday evening aboard the M/V June Aster, about 2.2km (1.3 miles) offshore.
The vessel had been around 4 nautical miles (7.4km) off the village of Turda near its destination of Coron when the fire was reported.
Video shared by the coastguard on Facebook showed much of the vessel engulfed in flames.
The ferry had sailed from Manila and was near Coron in Palawan province when the fire started.
Reports made no mention of the possible cause of the blaze, and the cause has not yet been determined.
Coastguard Captain Noemi Cayabyab told a local radio station on Thursday that 42 people had been rescued so far, according to the AFP news agency.
Cayabyab said conditions were still being assessed on Friday and rescuers intended to board the ferry once it was safe to do so.
“Based on the data we have right now on the rescued and the casualties, we still have 87 people who are unaccounted for,” she said, adding that the ship’s manifest had listed 134 passengers and crew.
“Just to make it clear, this is live data and may change, as our search and rescue operations are ongoing,” Cayabyab said.
“However, we have not yet been able to obtain information from the rescued individuals because we have not been able to speak with them,” she said, adding that attempts to put out the blaze were ongoing.
The Reuters news agency reported that 43 people were rescued as of Wednesday night.
Survivor Arnulfo Nokki Villanueva described the panic on board in a video broadcast by News5.
“The fire quickly spread. That’s when I dropped to the ground and my back was burned,” he said.
“I wanted to get a life jacket but failed to get one because people were stepping on me. People were in panic.”
Villanueva said he eventually escaped by jumping out of a window.
The coastguard, other government agencies, private volunteers and fishermen have been searching nearby waters, while coastal patrols have checked whether survivors may have drifted ashore. No new survivors or fatalities have been found.
The company said in a statement that it was coordinating with the coastguard and maritime officials to locate missing passengers, cooperating fully with the investigation into the fire’s cause and assisting those on board and their families.
Sea accidents are considered common in the Philippines, an archipelago of more than 7,000 islands regularly battered by monsoon rains and typhoons that can make travel conditions treacherous.
Poor vessel maintenance and overcrowding, and sometimes spotty enforcement of safety regulations, have also been blamed for past accidents.
A ferry carrying more than 350 people sank off the coast of Baluk-baluk island in January, killing at least 18.
The ongoing search for the 87 people still unaccounted for has kept rescue teams focused on the waters around the stricken M/V June Aster as authorities continue efforts to reach the vessel and investigate the cause of the fire.
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