The examination of Parchin is part of an inquiry by the International Atomic Energy Agency
into Iran's past nuclear activity. It is separate from inspections of other sites agreed to under July's deal between Iran and six world powers
, which are more focused on ongoing work.
Iranians were involved in collecting some of the samples from the sensitive military site, IAEA director general of Yukiya Amano said.
Earlier, a top Iranian official said that IAEA inspectors had not taken part in the sampling procedure at Parchin.
Iranian technicians took the samples and handed them to the IAEA, Atomic Energy Organization of Iran spokesman Behruz Kamalvandi was quoted in Iranian state media as saying.
But in a statement, the IAEA director general
appeared to clarify what had happened.
"As a result of experience gained over the years, the agency has, in certain circumstances, permitted states' representatives to carry out activities in support of the agency's verification work. This is done in a way that ensures that the agency's verification processes are not compromised," Amano said.
"In the case of Parchin, the Iranian side played a part in the sample-taking process by swiping samples," he said. "Authentication by the agency of the samples was achieved through use of an established verification process."
Amano said that the IAEA had monitored the process and that the samples had been taken to Vienna, Austria, where IAEA experts would analyze them.
Iran's potential involvement in the Parchin inspection was foreshadowed by the Obama administration in August.
A senior U.S. State Department official said that the IAEA would have "total oversight" of sampling and inspections of Parchin under an agreement between the agency and Iran over access to the site.
The official said Iran was "not self-inspecting" but would not deny that Iranian inspectors will "play a role" at the site.
Since Parchin is a military installation, Iran always has been adamantly against having foreign inspectors roaming around there.
Late last month, an IAEA report
indicating that Iran was in broad compliance with its nuclear commitments, but noting indications of construction activity at the Parchin site, was leaked to media outlets, including CNN.
The document -- part of the agency's routine review of Iran's program -- stated that the IAEA "has continued to observe, through satellite imagery, the presence of vehicles, equipment and probable construction materials."
On Monday, Amano said he had visited the site with his deputy Sunday.
"We entered a building which the agency had previously only been able to observe using satellite imagery," he said. "Inside the building, we saw indications of recent renovation work. There was no equipment in the building."
The specifics of the deal between the IAEA and Iran over the Parchin inspections have not been made public and are not included in this year's nuclear agreement, but Iran is required to satisfy the IAEA's concerns about its program
under that deal.
The conclusion of that inquiry is also a critical step in the implementation of international sanctions relief under the wider nuclear deal.