Fereydoun Abbassi, director of the Atomic Energy Organization of Iran, told the International Atomic Energy Agency in Vienna that power lines to the facility were severed using explosives just before a snap inspection.
Abbassi warned the IAEA that "terrorists and saboteurs" may have infiltrated its ranks.
"We must make director general of IAEA and his colleagues aware of this issue and give the necessary warning (to them)," he was quoted by Iran's semiofficial Fars News Agency as saying.
Abbassi said a similar attack struck the Natanz nuclear site but he offered few specifics.
He said targeting power to the nuclear sites was a way to damage centrifuge machines used to enrich nuclear material.
The IAEA said it wasn't able to verify that Iran was diverting nuclear material for military use. It had expressed concern, however, that parts of the nuclear program may have military dimensions.
Iran says it has the right to pursue a peaceful nuclear program under the nuclear Non-proliferation Treaty.
Former U.S. President George W. Bush authorized a program to target Iran's electrical and computer systems, The New York Times reports. Cyberattacks have struck parts of the Iranian nuclear program and some reports have linked those attacks to U.S. intelligence agencies.