Sulpicio Lines, the owner of Princess of the Stars, offered to fly one family member per victim to Manila from Cebu, where the ship was meant to dock, to help identify recovered bodies.
But the distraught relatives did not want to be moved.
In Manila, family members also waited anxiously.
"We want to see our relatives, even if they are dead already," said Rey Gilbuena, who had 18 kin on board.
Families are irate at the company for proceeding with a sailing when Typhoon Fengsen, with gusts of up to 195 kph (120 mph), had already hit the archipelago on Friday.
The government has ordered a review of maritime regulations and suspended Sulpicio's passenger ferry operations pending inspection.
The company has been involved in three other major shipping disasters in the past 21 years, including the world's worst peacetime sea tragedy in 1987 when the Sulpicio-owned Dona Paz ferry collided with an oil tanker killing more than 4,000 people.
Shipping tragedies are a common event in the Philippines, an archipelago of over 7,000 islands where safety rules are poorly implemented and substandard vessels ply dangerous waters.
Aside from the ferry disaster, possibly the worst in the Philippines in over 20 years, at least 155 people were killed, largely by drowning, in a torrent of floods in the south and centre of the archipelago, according to the Red Cross.
The sixth typhoon to hit the archipelago this year badly damaged the country's already shoddy infrastructure, washing away thousands of homes as well as roads and bridges.
In Iloilo, the province worst hit by Fengshen, over 200,000 people were forced to evacuate and local officials said it could take a week for two metre high floodwaters to recede.
Fengshen was expected to bring more rain to already flood-ravaged southern and eastern China as it makes landfall near Shantou in Guangdong province on Wednesday, according to the tropical storm monitoring website Tropical Storm Risk (http://tsr.mssl.ucl.ac.uk).
Authorities in the coastal province of Guangdong have ordered local governments to prepare disaster relief work.
