The 10,192-ton Superferry 14, carrying almost 900 passengers, had just left Manila for the central Philippines when the accident occurred shortly before 1:00 am (1700 GMT), the coast guard said.
Hundreds of people were plucked from the burning ship near Corregidor island on the mouth of Manila Bay by coast guard vessels and passing fishing boats which responded to the distress call.
Some of the injured arrived at the coast guard headquarters on the dockside with their faces almost burned beyond recognition. A line of waiting ambulances sped the victims away.
Christie Cayetona, one of the rescued passengers, recounted being woken up by a loud explosion from her bunk below deck.
"We rushed toward the main deck," she told Manila radio station DZRH by telephone aboard a rescue vessel. "There was smoke all over."
Coast guard Commodore Wilfredo Tamayo in his latest report said that of the 879 people passengers and crew, 112 remained missing, although operator Aboitiz Transport said 899 people were on board.
Aboitiz spokeswoman Gina Virtusio said the discrepancy will be "cleared up when we are able to match the names of those rescued and those in the manifest," Virtusio said.
Aboitiz had earlier said two passengers had died, but subsequently corrected the figure to only one.
Virtusio held up hope that those missing could still be alive.
"While the rescue was ongoing, the captain impressed to us that they all disembarked and were transferred to the vessels around," Virtusio said, adding "we have an anticipation that more (survivors) will be coming up."
Tamayo said search and rescue operations would continue into the dusk, but said investigators would not be able to penetrate the hull of the burned ship, which was still smouldering.
"We will be ready for search and recovery as soon as the situation permits the investigators to come in," he said. "Until now, there is still noxious gasses being emitted from the vessel. We have to wait until such time that we can (investigate)."
Tamayo declined to speculate whether some of those missing could have been trapped inside the ferry, which was towed to the waters near Bataan province, where it tilted and partly submerged in water.
President Gloria Arroyo ordered a thorough probe into the accident, the latest in a long list of sea accidents in the archipelagic Philippines.
"All the possible angles will be looked into," her spokesman, Ignacio Bunye said. "Let us wait for the results of the investigation. We do not wish to jump to premature conclusions."
The Superferry 14 was built to carry a maximum of 1,672 people, the company said. It had been in service for three years.
The fire was the latest mishap to hit the inter-island ferries that are the backbone of maritime transport here.
These ferries, often small, poorly maintained and overloaded, are vulnerable to sea collisions or sinking in rough water, resulting in several fatalities every year.
More than 4,000 people were killed in the world's worst peacetime maritime disaster when the Dona Paz ferry collided with an oil tanker off central Mindoro island in 1987.