On Wednesday, media reports stated that IAEA and Iran had a secret agreement, allowing Tehran to investigate and report on its controversial Parchin site.
"I am disturbed by statements suggesting that the IAEA has given responsibility for nuclear inspections to Iran. Such statements misrepresent the way in which we will undertake this important verification work," Amano said.
Amano stated that the IAEA-Iran roadmap agreements, agreed upon on the sidelines of Tehran nuclear talks, would be confidential.
"I can state that the arrangements are technically sound and consistent with our long-established practices. They do not compromise our safeguards standards in any way," Amano said.
Monitoring of suspected nuclear military sites is part of the deal Tehran made with the IAEA during the July nuclear talks.
Members of the United States intelligence community have claimed that the Parchin military facility was being used to develop a key component for a nuclear weapon delivery system.