The International Atomic Energy Agency didn't give a reason for the sudden resignation of Tero Varjoranta, stating Saturday that it doesn't comment on confidential personnel matters, the report said.
The IAEA conducts inspections in Iran to verify compliance with the terms of the deal. However, he noted that the organization would continue to "professionally" do their job.
Varjoranta, who was in the role for nearly five years, will be replaced by Massimo Aparo, an Italian nuclear engineer.
A permanent replacement will be appointed as soon as possible, the IAEA spokesperson said.
"As of today, the IAEA can confirm that the nuclear-related commitments are being implemented by Iran", IAEA Director General Yukiya Amano said in a statement.More news: CARLTON: A time to say thanks to mothers
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Since the accord was reached in 2015, the IAEA has carried out hundreds of inspections inside Iran.
The U.S. has repeatedly accused Iran of violating the spirit of the agreement secured in 2015 under the Obama administration, but the IAEA says it has no indications Iran has breached the agreement, the AP reported.
Under the JCPOA deal, the USA and other world powers agreed to lift some economic sanctions imposed on Iran in return for the latter agreeing to rein in its nuclear program.
The Trump administration faced worldwide criticism this week for its decision to exit the agreement, while Iran has stated it will attempt to negotiate the continuation of the deal among the remaining global signatories.
However, some analysts fear a collapse of the deal now that the USA has withdrawn and re-imposed sanctions on Iran, which may lead to Iran ending co-operation with the IAEA's inspections.