Four people were confirmed dead.
Three ships passing through the area picked up most of the 63 crew and passengers who survived, Lieutenant Commander Armand Balilo told reporters, as coast guard planes and helicopters joined in the search and rescue operations in waters off Verde island.
Our rescue teams found today four bodies, including two children, near the area where the ferry went down, Balilo said. We continue to scour the waters for possible survivors.
He said the Transportation Department has suspended the operations of the shipping company involved in the accident and ordered the inspection of all domestic ferries to avoid future accidents.
The roll-on, roll-off ferry was carrying at least 88 people and nine cargo trucks when it set off from Calapan on the central island of Mindoro for a two-hour trip to Batangas port on the main Luzon island late on Saturday, the coast guard reported.
About 30 minutes later, the ferry began listing after taking in water from its bow, Balilo said, adding it sank minutes later at about 1.6 nautical miles off Verde island.
It happened very fast, I was sleeping on a bench but soon found myself clinging on a floater (life ring), passenger Eric Musngi told a radio interview after a rescue ship brought some of the survivors to Batangas port.
There were dozens of people on the water crying for help and calling out the names of their family members and relatives. I don't know what happened to my mother and elder sister.
Some of the missing passengers may have gone down with the ship because there was very little time to alert everyone before it sank, Senator Richard Gordon, head of the Philippine National Red Cross, told reporters.
Based on my interviews with the rescued crew and passengers, the ship even failed to send out distress signals and to inform all those onboard about the ship's conditions, said Gordon. Many jumped into the water without life jackets.
On Thursday, at least three people died when a wooden-hulled ferry bound for the central island of Lubang collided with a fishing boat near the mouth of Manila Bay on clear weather.
About 24 are still missing and coast guard officials said they would investigate the accident.
Ferries are an important mode of transport in the Philippines, an archipelago of more than 7,100 islands, because they are affordable for the country's poor who comprise a third of the 92 million population. But accidents are common because of overcrowding, poor maintenance, and tropical storms.
(Editing by Rosemarie Francisco and Jerry Norton)