Labour Secretary Rosalinda Baldoz said the owners of Kentex Manufacturing had broken employment laws that were meant to guarantee minimum salaries, pensions and social security.
"They are not only illegal, they are immoral. This employer, they don't have a sense of social responsibility," Baldoz told AFP in an exclusive interview.
Seventy-two workers died when a fire tore through Kentex's two-storey factory, which produced cheap sandals and slippers for the local market, in an industrial district of the Philippine capital on Wednesday.
Nearly all of those killed were trapped on the second floor of the factory, with steel bars over windows ensuring they could not escape.
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The company had provided no fire safety training to their employers, according to survivors of the blaze, as well as victims' relatives and unions.
They also accused the company of paying salaries well below minimum wage, as well as withholding pensions, health benefits and other forms of social security.
Baldoz confirmed the company had used a "fly-by-night subcontractor" to hire casual workers, with the middle-man agency not paying required salaries and benefits.
After inspecting the site yesterday, Interior Secretary Mar Roxas hit out at the company's safety standards, stating that the welding should never have been done close to inflammable chemicals.
He also pledged to investigate why 69 of the 72 people killed had been trapped on the second floor behind steel bar-enclosed windows and with no viable fire exit.
Labour union leaders have also accused the government of being partly responsible for failing to carry out proper inspections that would ensure such companies were following labour laws.
About 50 labour union activists picketed the burned Kentex factory today, criticising the authorities and the factory management.
AFP was unable to contact management or spokespeople for Kentex.