Firemen said they counted 28 bodies but were only able to retrieve three as the gutted building threatened to collapse after the blaze, which began before noon (0400 GMT), destroyed the building.
"They were lying side by side, but all I could see were their bones," the Manila fire marshal, Senior Superintendent Sergio Soriano told AFP.
Rex Gatchalian, mayor of the industrial suburb of Valenzuela where the blaze occurred, told AFP before the death toll was announced that 67 workers were unaccounted for.
The fire sent a huge column of black smoke above the metropolis of 14 million people.
"I'm hoping against hope that they're still alive," Gatchalian said of the missing.
Gatchalian told wailing relatives outside the burning flip-flop factory earlier that none of those trapped inside had survived the fire.
Security guard Ardes said "more than 50" employees had punched in their time cards at his post by the gate earlier today before they began work.
Sparks from welding equipment used to repair a broken inner gate ignited flammable chemicals stored nearby, he added.
Fire engines lined the street outside as night fell, with firemen continuing to direct their water cannons at the blackened building, which was bathed with beams from search lights.
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