So far, 42 people have been rescued and efforts were ongoing, so the count of 87 people missing may change, coast guard spokeswoman Commodore Noemie Cayabyab said on Thursday.
The ferry MV June Aster had sailed from Manila and was near Coron in Palawan province when the fire started around 645pm on Wednesday.
Images from the scene showed the ferry was still on fire. Coast guard personnel tossed life jackets to survivors as the ferry burned in the background. Passengers were helped into smaller boats taking them to shallow water, and body bags were laid out at what looked like a port.
Bad weather and big waves were challenging rescuers. The ferry was around four nautical miles off Coron's village of Turda when it sent a distress signal but strong sea currents had dragged it to a distance of eight nautical miles off Turda.
Cayabyab said 134 people were on board, 117 of them passengers and 17 crew.
"Based on the data that we have right now, the rescued and casualty, we are still searching for 87 people," she told DZXL radio.
There was no information about any foreigners onboard, coast guard information officer Joy Gumatay told reporters.
Cayabyab said it was still unclear what caused the fire, and the coast guard is co-ordinating with the shipping company and maritime authorities to get more details.
Ferries are a common transportation method in the Philippine archipelago. Sea accidents are not uncommon due to storms, badly maintained vessels, overcrowding and spotty enforcement of safety regulations, especially in remote provinces.
In 1987, the ferry Dona Paz sank after colliding with a fuel tanker in the central Philippines, killing more than 4300 people in the world's deadliest peacetime maritime disaster.
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