Sixty-eight people are still missing after the ferry, MV St Thomas Aquinas, sunk in a collision with a cargo ship off the coast of Cebu province, 580 kilometres south of Manila, on Friday.
Authorities fear most of the missing were trapped in the 11,405-ton ferry, which was lying some 45 metres below the sea.
The coast guard said divers recovered 11 bodies from the St Thomas on Monday morning, but rough seas were slowing down the operations.
The ferry was carrying 870 people when it collided with the cargo ship MV Sulpicio Express 7 as they passed a narrow channel off the port of Talisay City.
The cargo ship's 38 crew members were unharmed, while 750 people on the St Thomas have been rescued, the coast guard said.