The ship has been out of radio contact for more than 24 hours and gale force winds are hampering rescue efforts. Officials on a nearby island have reported three survivors. They also said four bodies had been recovered.
The Red Cross estimates some 155 people have died across the country in floods and landslides caused by the storm. 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.