Rescue workers pulled dozens of corpses out of the ruins of the two-storey building in Manila, many of whom were believed to have been trapped on the second floor after the blaze broke out just after noon on Wednesday.
"Many of those retrieved were reduced to skulls and bones," national police chief Leonardo Espina said during an emotional press conference, as city authorities confirmed that 45 bodies had so far been found.
"Someone will definitely be charged because of the deaths. It doesn't matter if it's an accident, people died. Right now, we are investigating to clearly define what happened. For sure, someone will be charged."
Sparks from welding equipment used to repair a broken gate are believed to have caused the fire when they ignited flammable chemicals stored nearby.
The building, among a long row of factories in the rundown district of Valenzuela on the northern edge of the Philippine capital, made cheap slippers and sandals for the local market.
The footwear had names such as "Havana" that sound like well-known global brands, company employees said.