Obama cancelled a meeting with Duterte after the firebrand leader unleashed a barrage of criticism of the US president, saying he would not be lectured about human rights over his crackdown on narcotics, which has seen police and shadowy assassins kill nearly 3,000 people.
The crackdown has seen Duterte's domestic popularity soar but has prompted widespread international condemnation from the United Nations and human rights watchdogs, and the American Chamber of Commerce in the Philippines said it was also damaging investor sentiment.
The US is the Philippines' largest trading partner after China, and a key source of foreign direct investment.
The traditionally strong ties between the US and the Philippines have been "strained by language from Philippine leaders" which is also creating "investor concern," the statement said.
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Relations saw a spectacular setback this week when Duterte branded Obama a "son of a whore" after being told the US president planned to raise concerns about his war on drugs.
The high-profile spat "could harm the long-standing optimism of American business to invest in the Philippines," the chamber of commerce added.
Duterte was elected to office in a landslide this year after pledging to kill 100,000 people in an unprecedented war on crime.
He vowed in the campaign that so many bodies would be dumped in Manila Bay that the fish there would grow fat from feeding on them.