The State Department, however, said the 56-year-old Feeley had retired due to personal reasons.
Feeley, a former Marine Corps helicopter pilot, is the first career foreign service diplomat to resign under Trump.
"John Feeley, the US Ambassador to Panama, has informed the White House, the Department of State, and the Government of Panama of his decision to retire for personal reasons, as of March 9 of this year," the State Department said.
"Deputy Chief of Mission Roxanne Cabral will assume leadership of our diplomatic mission in Panama until a new Ambassador arrives," it said.
According to multiple media reports, Feeley in his resignation letter said that he cannot serve under the current US president.
"As a junior foreign service officer, I signed an oath to serve faithfully the president and his administration in an apolitical fashion, even when I might not agree with certain policies," Feeley said in his letter reported by various media outlets.
"My instructors made clear that if I believed I could not do that, I would be honor bound to resign. That time has come," he said.
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