Yukiya Amano held morning talks with Foreign Minister Mohammaf Javad Zarif before meeting President Hassan Rouhani, Iran's official IRNA news agency reported.
Addressing the allegations, long denied by Tehran, would be an important element in the comprehensive deal on Iran's nuclear programme that world powers are seeking to reach by November 24.
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But it comes shortly before an August 25 deadline for Iran to provide the IAEA with information to clear up some of the many claims of past and possibly ongoing research into nuclear weapons.
As part of the implementation of the interim deal it struck with world powers last November, Iran handed the IAEA documents in April and May relating to its past research, the first time it had done so in six years.
Amano welcomed the move but warned in June that the information would take time to assess and that the IAEA had further questions about the research, most of which was conducted more than a decade ago.
Iran says that its research into sophisticated explosive detonators, which can be used to set off a nuclear warhead but also have other applications, was for peaceful civilian ends.
The research is one of a dozen alleged "possible military dimensions" to Iran's nuclear programme that the IAEA has been investigating for years.
Iran has always dismissed the allegations as being based on hostile intelligence provided by the US Central Intelligence Agency (CIA) and Israel's Mossad and had long refused to grace them with a reply.
Iran denies seeking or ever having sought to develop nuclear weapons, insisting that its nuclear programme is for peaceful purposes only.
Amano's visit comes ahead of a new round of talks between Tehran and the major powers expected before the UN General Assembly starts on September 16.
The talks are aimed at securing a historic accord under which Iran scales back its nuclear activities to allay Western concerns about its ambitions.
In return, Iran would be granted relief from painful Western sanctions.
The deadline is November 24, a year after the interim deal was struck in Geneva partially freezing Iran's nuclear activities in return for minor sanctions relief.
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