Duterte had given the airline a Friday deadline to pay arrears.
“The (Department of Transportation) has accepted the offer of PAL to pay in full the six billion-peso claims of the (Civil Aviation Authority of the Philippines/Manila International Airport Authority,” a joint statement said.
“One of the overriding reasons why PAL agreed to settle is to manifest its trust and confidence in President Duterte’s administration,” the statement said.
The airline also committed to “keep all transactions updated and current” with the aviation and airport authorities, it added.
On September 26 Duterte said he had told PAL chairman and billionaire Lucio Tan: “You are using government buildings, airport, you have back debts for the use of the runway that you have not paid.
“I said, ‘You solve the problem yourself. I will give you 10 days. Pay it. If not I will close it down. No more airport’.”
Previously state-owned PAL was sold off in 1992, and the government said the fees were waived when the airline was government-owned.
Despite an increase in low-cost competitors, PAL still has the largest fleet in the Philippines and is the only local carrier to fly to North America and Europe.
In June it said it planned to increase its fleet serving smaller islands in the archipelagic nation.
PAL’s parent company, PAL Holdings, suffered a net loss of 501 million pesos for the three months to June due to higher fuel costs and aircraft lease charges.