International Atomic Energy Agency chief Yukiya Amano's visit comes as a December 15 deadline looms for the completion of the watchdog's long-running inquiry into allegations that at least until 2003, Iran conducted research into how to build a bomb.
Iran has said the accusations -- including that it carried out explosives tests at the Parchin military base -- are groundless and based on malicious intelligence provided by its enemies.
Amano held talks with Foreign Minister Mohammad Javad Zarif and President Hassan Rouhani as well as atomic agency chief Ali Akbar Salehi, Iranian media reported.
Amano will also address a 12-member committee set up by the Iranian parliament to examine the deal, a spokesman for the panel told state television.
"The visit will focus on... Clarification of past and present outstanding issues regarding Iran's nuclear programme," the IAEA said ahead of Amano's trip.
On September 9, the UN agency said Iran must resolve "ambiguities" over its past nuclear activities before crippling UN and Western sanctions can be lifted.
Iranian lawmakers are in the final stages of reviewing the text of the nuclear agreement. It is not clear whether there will be a vote or not.
Earlier this month in the United States, the Republican-led House of Representatives rejected the nuclear deal in a purely symbolic vote held a day after the Senate cleared the way for the accord to come into force.
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