Pulitzer-Prize winner Seymour Hersh reported that covert operations to identify as many as 36 or more nuclear, chemical and missile potential targets in Iran have been carried out by U.S. Special Forces. By defining these as military missions, the Bush administration hopes to evade legal restrictions imposed on the CIA's covert activities overseas.
There are satellite photographs showing disputed nuclear facilities near Natanz and Arak.  The International Atomic Energy Authority (IAEA) inspected these sites in early 2002 without finding conclusive evidence of military use, though traces of highly enriched material were found.
The covert missions have been ongoing for nearly a year, and have taken place in as many as ten Middle Eastern and South Asian nations. In return for his country's assistance, Pakistani President Pervez Musharraf is said to have received assurances that the US government will not demand for questioning Abdul Qadeer Khan, Pakistani nuclear scientist and creator of their nuclear bomb.
The Pentagon has strongly criticised the report, though without explicitly denying the existence of covert operations in Iran. According to the Pentagon spokesman "Mr. Hersh's article is so riddled with errors of fundamental fact that the credibility of his entire piece is destroyed."
He went on to state: "Mr. Hersh's source(s) feed him with rumor, innuendo, and assertions about meetings that never happened, programs that do not exist, and statements by officials that were never made."

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U.S. reported to mount covert operations in Iran