The AEOI said in a sttaement on Wednesday that the female monitor left her mission unfinished and flew out of Iran after security staff at the Natanz uranium enrichment site denied her entry, Press TV reported.
"As it is protocol, all of the IAEA inspectors' belongings are closely inspected and scanned before they enter any of the country's nuclear facilities," the AEOI said.
"Upon this lady inspector's entry, the security control machines sounded the alarm and denied her entry," it added, noting that Iran had reported the issue to the IAEA.
Iran also told the UN nuclear agency in a report that the inspector's previous admissions at various sites were all scrapped and as a result, she decided to abort her mission and go back to Vienna.
The report also asked the agency to help with investigations into the matter and it accepted.
"The investigations are ongoing," the AEOI said, adding that the Iranian mission at the IAEA would present it with a comprehensive report on the matter on Thursday.
Iran began enriching uranium in the Fordow facility at midnight Wednesday by feeding the centrifuge machines with uranium hexafluoride (UF6) in the fourth step of reducing its commitments to the 2015 nuclear deal.