Most of the mines targeted by the order produce nickel and account for half of the Philippines' world-beating exports of the raw material used to make steel.
Environment Secretary Gina Lopez, a staunch mining critic, said 23 mines had been told to close after illegally encroaching on watersheds, leaking waste into rivers and destroying trees.
A further five mines have been ordered to suspend their operations, while the decision on another mine has been deferred.
"No amount of money warrants the life of the Filipino. I don't care. That's water."
President Rodrigo Duterte threw his support behind Lopez's crackdown, saying: "I support her. She (has) pro-people, pro-poor policies."
The Philippines is the world's top supplier of nickel ore and the main exporter to China, and the move is expected to fuel a rally in global prices.
In 2015 the Philippines produced about 24 percent of the nickel consumed worldwide, according to Morgan Stanley.
The Chamber of Mines of the Philippines, an industry group, warned the decision would hurt the country's nickel production and could discourage investment in the industry.
It also accused Lopez of not giving miners an opportunity to address the audit findings.
The move risked "sending signals out to the market and to mining investors that they are not welcome here", Ronald Recidoro, the chamber's vice president for legal and policy affairs, told AFP.
Mining stocks fell on Lopez's announcement, including Nickel Asia, one of the world's largest nickel producers, which fell 0.58 percent to 6.81 pesos, up slightly from the intra-day low of 6.61 pesos.
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