The mining industry -- accused of illegal tree felling and polluting rivers -- has also questioned the order of Environment Secretary Gina Lopez.
The Philippines is the world's top supplier of nickel ore and the main exporter to China. The order has already caused a rise in global nickel prices and a fall in local mining shares.
"I don't think (Lopez) did it arbitrarily but anything like this would need a response like more scientific and data-driven studies," said Socioeconomic Planning Secretary Ernesto Pernia.
Lopez, a staunch mining critic, said last week that 23 mines had been told to close after illegally encroaching on watersheds, leaking waste into rivers and destroying trees. A further five mines had been ordered to suspend operations.
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Finance Secretary Carlos Dominguez, on his official Twitter account, also expressed misgivings, saying: "I am deeply concerned over the welfare of the 1.2 million people affected by the closure of the 23 PH (Philippine) mines. This will result in joblessness."
The closures would also hit local government tax revenues, he said.
Duterte, who enjoys wide popular support, has backed Lopez's order even as reports say the mining industry may challenge it in court.
In a statement today, Lopez said she would outdo the industry, declaring "give me... Maximum of two years. I will prove that a green economy can create more jobs than mining could ever create."
She also said mine workers would not end up unemployed but would be found jobs in mine rehabilitation and reforestation.
"My issue is not about mining, my issue is about social justice," she said.
She also cited "mounting concerns over new environmental and social requirements, and their potential to drive up the costs of compliance" in the nickel industry.
"The prospect of higher operational costs could well impact the commercial viability of some projects," the Singapore-based Taylor said.
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