Nine people died when the SuperFerry 9 listed then sank, but more than 900 were rescued from life rafts near the southern city of Zamboanga.
Officials are hopeful some passengers may still be drifting in life rafts.
The Philippine defence minister said the rescue had been helped by the presence of other vessels nearby.
A spokesman for the ferry owner, Aboitiz Transport System, said the priority was to find survivors.
"The focus of the company now, in co-ordination with the authorities, is the rescue and the proper counting of the survivors," said Erden Ferrer.
"That is actually the primary objective we have at the moment."
He said the company was finding out what happened to the crew.
"The captain is alive. The captain is on board the Navy Ship 116, at the moment; that we have confirmed.
"And also, about the 113 crew, we're still verifying the number and the whereabouts of the crew."
The company earlier said that the crew were the last to leave the ship at 0842 local time, when the ferry finally sank.
It also said that local rescue units and the Philippine National Red Cross were searching the coastal towns near the area for survivors.
The SuperFerry 9 began listing about 0203 local time on Sunday (1830 GMT Saturday) during its journey from General Santos to Iloilo, and all on board were ordered onto life rafts when it became apparent that the problem could not be fixed.
The coastguard, the navy, the air force and private boats in the area rushed to help.
The death toll could rise if reports of more fishing boats bringing in dead bodies proved accurate, officials said.
The Philippine air force and army have sent helicopters to help in the search for those still missing.
The cause of the sinking was unknown, but the weather was reported to be fair at the time of the incident.
The ferry ran into trouble about 530 miles (860km) south of the Philippine capital, Manila.
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