The 23,824-tonne ferry has a passenger capacity of 1,992.
There is some confusion over the number of people on board. Officials initially reported it was carrying 747 passengers and crew, but on Monday said there were 100 more.
Anxious relatives have gathered at the shipping company's office in the capital
The Philippine President, Gloria Arroyo, has demanded an explanation as to why the ferry was allowed to leave port on Friday despite warnings that a typhoon was about to hit.
"Why did you allow it to sail and why was there no ample warning? I want answers," she told civil defence and coast guard authorities during a briefing on the accident.
Worried relatives have been gathering at the offices of Sulpicio Lines.
One relative, Lina Salinas, said she had waved off her sister on the 22-hour voyage on Friday.
"We knew it was signal number 1 [the first stage of typhoon alerts] at the time, but we were not really worried because it was not raining here at all," Ms Salinas was quoted by AFP news agency as saying.
A spokesman for the company said the priority was the search and rescue operation and that there would be no talk of responsibility at present.
Typhoon Fengshen swept across the central Philippines on Saturday.
PHILIPPINES' WORST FERRY DISASTERS
1987: More than 4,300 people die when the Dona Paz ferry collides with an oil tanker off Mindoro island - the world's worst peacetime shipping disaster
1988: Dona Paz's sister ship, Dona Marilyn, sinks off Leyte province, killing 250-300 people
1994: About 140 people die when a freighter hits the Cebu City ferry in Manila Bay
1998: The Princess of the Orient ferry sinks near Batangas province, leaving 150-200 people dead
2004: A fire aboard the Superferry 14 vessel kills 116 people, near Manila Bay. Abu Sayyaf claims it planted a bomb on board
In Iloilo, a central province where 101 people were reported dead or missing, chief administrator Manuel Mejorada said most of the victims had been killed as a result of flooding caused by the storm.
"Yesterday there was hardly any villages and communities which were not under water, and where the people were literally stranded on rooftops with no food and no water, and chilling in the cold.
"Right now the floodwaters have receded, and we are shifting our efforts to bringing food, water, medicine and clothing," he told the BBC.
At its peak, the storm was packing gusts of up to 93mph (150 km/h). It changed course on Sunday, hitting the capital Manila with heavy rainfall at dawn.
Thousands of people across the country have been evacuated from their homes. Many roads are blocked and there have been widespread power cuts.
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