Justice Secretary Vitaliano Aguirre announced the inquiry as firemen prepared to enter what remained of the NCCC mall in the southern city of Davao where they hope to retrieve those who perished in Saturday's blaze.
The fire compounded the Christmas misery in the south of the mainly Catholic nation where tens of thousands were also displaced by floods and landslides from a storm that also killed more than 200 others on Friday.
"The loss of lives and the resulting damage... underscore the need to determine if someone is at fault and should be held criminally liable," Aguirre said in a statement.
Deadly blazes occur regularly in the Philippines, particularly in slum areas where there are virtually no fire safety standards.
Relatives of the missing said many of those still unaccounted for were staff from a call centre for the US-based market research company SSI that occupied the building's top floor.
Local authorities yesterday said no-one trapped in the fire would have survived but firemen have only managed to retrieve one unidentified body so far.
The Davao fire marshal had yesterday described the shopping mall as "an enclosed space with no ventilation", though the authorities said they had yet to determine the cause of the blaze.
"There is no truth to that allegation. In fact as per accounts of those who got out, they were able get out thru the fire exit," Thea Padua, the mall's public relations officer, told AFP by text message.
Some relatives of those missing criticised rescuers for what they felt was the slow pace of recovery efforts.
"They seem so relaxed," said Jolita Basalan, weeping as she waited for news of her missing 29-year-old son Jonas who worked at the call centre.
But authorities earlier told AFP that firemen needed to inspect the structural integrity of the burnt-out building before venturing inside its gutted remains.
Corruption and exploitation mean supposedly strict fire standards are often not enforced in the Philippines.
In 2015, a fire tore through a footwear factory in Manila, killing 72. Survivors of that blaze blamed barred windows and other sweatshop conditions for trapping people inside the factory.
In the deadliest fire in the Philippines in recent times, 162 people were killed in a huge blaze that gutted a Manila disco in 1996.
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