The UN watchdog said that it had so far found no evidence Iran was trying to develop atomic weapons, but also said it was not ready to certify that Tehran's nuclear program was exclusively peaceful.
Iran acknowledged in a letter to the IAEA last month that it had carried out "plutonium separation experiments" between 1988 and 1992, the agency said in a confidential report released Monday.
"Neither the activities nor the separated plutonium had been reported previously to the agency," said the report, a copy of which was made available to AFP.
The report, which is to be submitted to a meeting of the IAEA's 35-nation board of governors next week, outlines almost two decades of deception by the Islamic republic over its nuclear activities.
However, the report also credited Iran for having since October adopted a policy of "full disclosure."
The IAEA said that "according to Iran, a total of about seven kilograms of UO2 (depleted uranium) was irradiated, three kilograms of which was processed to separate plutonium."
"Iran stated that these experiments had been carried out to learn about the nuclear fuel cycle, and to gain experience in reprocessing chemistry," the report said.
Iran also acknowledged enriching uranium between 1991 and 2002.
It had used 1.9 kilograms of imported uranium UF6 gas that it had tried to hide from international inspectors by saying it had disappeared through evaporation from "leaking valves on the cylinders containing the gas."
"Iran has now acknowledged that it has been developing, for 18 years, a uranium centrifuge enrichment program and for 12 years, a laser enrichment program," the report said, referring to technologies that produce nuclear fuel for reactors but also material for making atomic weapons.
It said Iran had made "limited quantities of nuclear material" that "dealt with the most sensitive aspects of the nuclear fuel cycle, including enrichment and reprocessing."
The report said Iran had "concealed many aspects of its nuclear activities with resulting breaches of its obligation to comply with the provision of the safeguards agreement" of the nuclear Non-Proliferation Treaty (NPT).