Duterte's volatile nature threatens to complicate Washington's ties with its closest ally in Southeast Asia as it tries to forge a united front in the region in response to China's extensive claims in the strategic South China Sea.
The Philippines has been central in this effort due to an international court case it brought and won against Beijing.
In March, the United States and the Philippines agreed on five locations for U.S. military facilities in the country under a new security deal. The deal grants Washington increased military presence in its former colony through rotation of ships and planes for humanitarian and maritime security operations.
Asked about Duterte's comments, U.S. Secretary of Defense Ash Carter said the defense relationship with the Philippines was a "strong" and "longstanding" one.
Speaking to reporters, Carter also described the Philippines' new defense minister, Delfin Lorenzana, as someone who was "very knowledgeable about all the things that we do together."
An official of the U.S. State Department said "government to government" relations with Manila remained strong.
"The areas that we believe we have robust, strong cooperation with them, we are not going to just simply throw that aside."
The official noted that Duterte was new to national leadership having served as a city mayor.
"He is maybe feeling his way into the new job," the official said.
Former U.S. officials said China would be pleased by the U.S.-Philippines friction.
"Time will tell whether President Duterte steps back from this episode and realizes he needs to recalibrate his choice of words in engaging U.S. leaders," said Amy Searight, a former senior Pentagon official now at Washington's Center for Strategic and International Studies think tank.
Evan Medeiros, Obama's former top Asia adviser and now a senior analyst at the Eurasia Group, saw the row as a "speed bump, not a road block" in U.S.-Philippines ties.
"It's unfortunate, but doesn't fundamentally derail the relationship," he said.
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