"I confirm that a team of IAEA inspectors is today conducting an inspection at Parchin, including the taking of environmental samples," spokesman Mark Gwozedecky said on Thursday.
Environmental samples are swipes taken to check for radiation. Results from such sampling are available after about a month of laboratory analysis.
Iran had warned on Wednesday that it would not tolerate "spying" at the Parchin military facility, which had been off limits to IAEA inspectors.
The IAEA visit coincides with the resumption of EU talks in Brussels on a trade accord with Iran, 18 months after they were suspended due to concerns about Tehran's nuclear plans.
The negotiations on a trade and cooperation agreement were restarted after Iran agreed to suspend uranium enrichment, the crucial part of the nuclear fuel cycle that can also make material for atomic bombs, in an accord thrashed out following intense pressure, notably from the United States.
But the resumption was clouded by a reported announcement from Tehran that Iran plans to resume uranium enrichment soon.
Iran said it planned to resume
uranium enrichment soon
Iran has consistently claimed it is only giving up enrichment voluntarily as a confidence-building measure and reserves the right to enrich uranium when it wishes.
The IAEA team arrived in Tehran on Wednesday and is to stay in the country for a week, student news agency ISNA reported.
Tehran gave permission for inspectors to take environmental samples from the massive Parchin site about 30km southeast of Tehran to disprove US allegations of secret weapons-related activities.
Washington has voiced concern that the Iranians may be working on testing high-explosive charges with an inert core of depleted uranium at Parchin as a sort of dry test for how a bomb with fissile material would work.
Tehran has denied carrying out any nuclear-related work at the site and insists its nuclear drive is aimed at generating electricity.
"We have allowed inspections into our military installations
but we will not allow
any espionage or the theft of information
from our military sites"
spokesman for Iran's nuclear negotiations team
"We are watchful. We have allowed inspections into our military installations but we will not allow any espionage or the theft of information from our military sites," Hossein Mousavian, the spokesman for Iran's nuclear negotiations team, said in remarks carried by the Mehr news agency on Wednesday.
"It is not necessary for the inspectors to enter the installations. They are authorised to take samples outside (the buildings) using their equipment."
Parchin is an example of a so-called transparency visit where the IAEA is going beyond its mandate under the nuclear Non-Proliferation Treaty to check if nuclear materials have been diverted away from peaceful use.
IAEA chief Muhammad al-Baradai announced last week that Iran had finally given the green light for his inspectors to investigate Parchin after seeking access to the site since July.