Richard Johnson, the assistant coordinator for Iran nuclear issues at the Office of Nuclear Implementation, reportedly handed in his resignation this week.
A civil servant, Mr Johnson had been involved in failed negotiations including the UK, France and Germany to save the deals after Mr Trump threatened to pull out.
Mr Johnson did not give an exact reason for his resignation but in an email circulated to colleagues and staff and obtained by Foreign Policy, he said the 2015 agreement with Iran had proved to be successful.
He wrote: “I am proud to have played a small part in this work, particularly the extraordinary achievement of implementing the [deal] with Iran, which has clearly been successful in preventing Iran from acquiring a nuclear weapon.”
According to his LinkedIn profile, Mr Johnson had worked as a non-proliferation officer in the US State Department since June 2006. He served as an assistant coordinator for Iran nuclear issues from June 2015.
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Writing on Twitter, Laura Kennedy, a former ambassador and a board member of the Centre for Arms Control and Non-Proliferation, said: “Richard Johnson is among the best and the brightest. His departure from the [US government] is part of the huge, worldwide collateral damage that is being wrought by Trump’s violation of the Iran deal. Feels like 2003 all over again.”
On Tuesday Mr Trump ended the US’ commitment to the Joint Comprehensive Plan of Action (JCPOA) negotiated between Iran, the EU, US, Russia, China, France, Britain, and Germany, which was signed by his predecessor Barack Obama in 2015.
It set limits to Iran’s stockpile of enriched uranium, which can be used to make reactor fuel but also nuclear weapons, until 2031. It also limits the number of centrifuges that can be installed to enrich uranium until 2026.
Iran also agreed to modify a heavy-water facility so it could not produce plutonium suitable for a bomb.
In return, Iran was allowed to trade with other countries.
As he pulled the US out of the deal, Mr Trump said it was “decaying and rotten”, adding that it was “an embarrassment” to him “as a citizen”.
Mr Johnson’s departure leaves a growing vacuum of experts on Iran’s nuclear programme in the US State Department, according to Foreign Policy.
One US official told the news website Mr Johnson’s resignation was a “big loss” for the department and was symbolic of a growing sense the Trump administration was sidelining career experts on foreign policy issues.
The chief of inspections at the UN’s nuclear watchdog also resigned suddenly on Friday, the agency announced without giving a reason.
Mr Varjoranta, a Finn, had been a deputy director general of the International Atomic Energy Agency (IAEA) and head of its department of safeguards, which verifies countries’ compliance with the nuclear non-proliferation treaty, since October 2013.
He will be replaced in an acting capacity by the head of the department’s Iran team, the Vienna-based IAEA said.