The ferry, MV Thomas Aquinas, began sinking after hitting the cargo vessel on Friday evening near the central city of Cebu, officials said.
Coastguard and naval vessels were joined by local fishing boats in the rescue effort, which is continuing.
With so many still unaccounted for, it is feared the death toll could rise.
The ferry, carrying 692 people, was sailing into the port at Cebu – the country’s second biggest city – when it collided with the cargo ship travelling the other way at about 21:00 local time (01:00 GMT).
“The impact was very strong,” Rachel Capuno, a spokesperson for the owners of the ferry, told local radio.
She said the ship sank within 30 minutes of the collision, the AFP reports.
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