"Based on all information currently available to the agency, it is clear that Iran has failed in a number of instances over an extended period of time to meet its obligations under its safeguards agreements" from the nuclear Non-Proliferation Treaty (NPT), said the report.
The report was written by IAEA chief Mohamed ElBaradei ahead of an IAEA meeting next week that will decide whether Iran should be cited for hiding an alleged nuclear weapons program.
A ruling of Iranian non-compliance with nuclear Non-Proliferation Treaty (NPT) safeguards agreements could lead to UN sanctions against Iran.
In September, the IAEA had imposed an October 31 deadline on Iran to answer all its questions about its nuclear program.
The report said Iran had since October 16 "adopted a policy of full disclosure and decided to provide the agency with a full picture of all its nuclear activities."
"Since that time Iran has shown active cooperation and openness. This is a welcome development," the report said.
In a clear move to avoid sanctions, Iran had on October 23 provided, only eight days before the deadline fell, what it said was a full report on its nuclear program to the IAEA.
Previous to that Iran had "concealed many aspects of its nuclear activities with resulting breaches of its obligation to comply with the provision of the safeguards agreement."
It said that until October, Iran's cooperation had been "limited and reactive."
The safeguards failures included testing uranium enrichment with centrifuges, something the IAEA caught Iran doing when it did environmental sampling in the past few months at a suspect site.
The IAEA discovered "the use of imported natural uranium hexafluoride for the testing of centrifuges at the Kalaye Electric Company (near Tehran) in 1999 and 2002, and the consequent production of enriched and depleted uranium," the report said.
Enriched uranium can be a fuel for nuclear reactors but can also be used to make atomic weapons.
The report said Iran had also failed to report "the import of natural uranium in 1994."
The end result is that Iran has secretly developed a nuclear program with "a practically complete front-end of a nuclear fuel cycle, including uranium mining and milling, conversion, enrichment, fuel fabrication, heavy water production, a light water reactor, a heavy water research reactor and associated research and development facilities," the report said.