Duterte is battling militants in the southern city of Marawi, while rights groups have accused him of orchestrating a crime against humanity with police killing more than 3,800 drug suspects in 14 months.
"The re-emergence of conflict in the southern Philippines, as well as the Duterte administration's focus on the eradication of illegal drugs, represents a rising but unlikely risk of a deterioration in economic performance and institutional strength," the credit ratings agency said.
But martial law, imposed by Duterte on the southern region of Mindanao to stop the Islamist threat, could be declared elsewhere in the country and upset this balance, it said.
"(A) worsening of the Islamist insurgency in Mindanao... could lead to an expansion of martial law, undermine both foreign and domestic business confidence, and disrupt economic activity in other parts of the country," it said.
However yesterday Defence Secretary Delfin Lorenzana warned Duterte may also declare nationwide martial law if threatened protests against his rule turned violent or disrupted the country.
Anti-Duterte protests are planned for September 21, the 45th anniversary of the imposition of martial law by the late dictator Ferdinand Marcos, who was ousted in a bloodless "People Power" revolution in 1986.
Moody's also cited "continued uncertainties" over Duterte's proposed comprehensive tax reform law that Congress had yet to pass.
The report affirmed Moody's short-term 6.5 per cent GDP growth forecast for the Philippines this year and 6.8 per cent in 2018.
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