Such sampling is usually done by the International Atomic Energy Agency's own experts.
But IAEA chief Yukiya Amano told reporters that Iranians carried out that part of the probe at Parchin, where the agency suspects that explosive triggers for nuclear weapons might have been tested.
The arrangement was first revealed in confidential draft agreement between the sides seen last month by The Associated Press.
Iran's atomic energy agency spokesman, Behrouz Kalmandi, said IAEA experts were not physically present during the sampling. But Amano said the procedure meets strict agency criteria that ensure "the integrity of the sampling process and the authenticity of the samples."
Amano spoke a day after he was taken on what Iranian media described as a ceremonial tour of the military site. He told reporters in Vienna that he was able to enter a building that the agency had been observing via satellite and saw signs of "recent renovation work."
Amano's one-day visit to Iran is part of an assessment due in December that will feed into the nuclear deal reached in July between Tehran and six world powers and will help to determine whether sanctions will be lifted.
Iran denies it has ever sought nuclear weapons, and insists Parchin is a conventional military site. Tehran has refused to allow inspections of its military sites as part of the nuclear deal, fearing foreign espionage.
Under the July agreement, Iran would curb its nuclear activities and submit to new inspections in return for billions of dollars in sanctions relief.
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