About 90 Iranian and foreign journalists were also shown round the site, where employees in white overalls and face masks feed uranium "yellow cake" into a conversion line.
"All these journalists can see and tell the world that Iran's activities are peaceful," Ali Asghar Soltanieh, Iran's IAEA envoy, said during the tour.
Soltanieh said the trip showed Iran's "transparency" and pointed out two IAEA cameras to monitor work in a room were UF6 is produced at the site, situated in a barren area southeast of Isfahan and surrounded by anti-aircraft guns.
The United States has said putting Iran's nuclear activities on display would not build confidence abroad.
The envoys, who stay in Iran until Monday, are not due to visit the Natanz uranium enrichment site where UF6 gas is fed into centrifuges to make power plant fuel or, if greatly enriched, material for warheads.
The group comprises ambassadors from Egypt, Malaysia, Cuba, Algeria and Sudan, and a Syrian representing the Arab League.
"They are not technical people and will not be able to pass judgment on what is going on. This is a publicity exercise, that's the main point," a NAM ambassador in Vienna, where the IAEA is based, said ahead of the visit.
The IAEA says it needs more information about Iran's atomic work before it can give a clean bill of health and has urged Iran to reconsider a move to bar 38 out of 200 inspectors whose role is to check whether materials are diverted to bomb making.
Iran blocked the inspectors after the United Nations penalised Tehran last month for refusing to halt enrichment.
The UN sanctions bar the transfer of sensitive materials and know-how to Iran's nuclear programme.