Mohamed ElBaradei, who arrived on Saturday, will discuss plans to allow International Atomic Energy Agency (IAEA) inspectors to visit the site in Qom, as demanded by world powers.
He is scheduled to meet Ali Akbar Salehi, the head of the Islamic republic's atomic energy organisation on Sunday.
Iran agreed to allow IAEA inspectors unfettered access to the plant during talks with the permanent members of the UN Security Council plus Germany in Geneva earlier in the week.
But Ali Shirzaidan, the Iranian atomic organisation's spokesman, said ElBaradei's two-day visit had "no connection" with western governments' condemnation of the news Tehran was building a second enrichment plant.
Speaking to the Fars news agency, Shirzadian noted that ElBaradei's visit was planned prior to the Geneva talks.Shirzaidan was also reported as saying ElBaradei would discuss "more co-operation" and how fuel could be provided for Tehran's research reactor.
Iran's English-language Press TV reported that ElBaradei would not visit the Qom facility during his trip.
Western powers suspect Tehran is making an atomic bomb under the guise of its civilian nuclear work.
Source: Al Jazeera (English)