Of the 831 people aboard the St. Thomas Aquinas, 629 have been rescued, the service said.
There were 664 passengers and 116 crew members on the ferry when it sank in more than 100 feet of water after colliding with the Sulpicio Express 7 about 10 p.m. Friday off Cebu in the center of the Philippine archipelago.
The Philippines News Agency had earlier reported 752 passengers and 118 crew members were on the ship.
Philippine naval and coast guard vessels, a C-130 aircraft, private fishing boats and a Malayan tugboat were involved in the search and rescue effort, the coast guard said.
Rear Adm. Luis Tuason Jr. said specialist divers recovered four more bodies Saturday from inside the ferry, increasing the death toll. Two sea marshals who were traveling on the Aquinas were among the missing, a coast guard spokesman said.
Tuason said the coast guard was trying to contain spilled oil from the collision, the Sun Star Cebu in Cebu City reported.
Some of the hundreds of survivors were at the ferry terminal and in hotels in Cebu City, officials said. Others were given shelter at a chapel in Talisay City.
All Sulpicio Lines and 2GO Shipping Lines vessels were grounded Saturday by order of the Maritime Industry Authority (MARINA) so they could be inspected, the Philippine Star reported.
MARINA chief Maximo Mejia Jr. said "there was no reason to believe that the incident has anything to do with questions of stability of structural integrity of the ships." However, he said all the ships would be inspected to ensure their trustworthiness.
Any of the lines' ships now at sea would be inspected on their return, he added.
Pope Francis sent a telegram of condolence to Cebu Archbishop Jose Palma, GMA News reported.
The message, written by Vatican State Secretary Cardinal Tarcisio Bertone, said the pope "was deeply saddened by the tragic loss of life."