The career diplomat announced his plans to step down in a private Facebook post to his friends on Friday, according to the Foreign Policy publication.
"For the President to say the EU was ‘set up to take advantage of the United States…’ or that ‘NATO is as bad as NAFTA’ is not only factually wrong, but proves to me that it’s time to go," he reportedly wrote.
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Melville has served as a diplomat for 33 years under six US presidents and 11 secretaries of state. His stint in Estonia, a small Baltic nation in Eastern Europe, began three years ago.
Transatlantic relations hit their lowest point following the recent G7 summit, as Donald Trump blamed his partners and allies for taking advantage of the US in terms of trade.