The find heightened concerns that Tehran may be running a secret nuclear weapons program.
Agency inspectors found "particles" of highly enriched uranium that could be used in a weapons program at the facility at Natanz, said the diplomat, who covers agency activities.
The United States has accused Iran of developing a clandestine nuclear weapons program, violating the Nuclear Nonproliferation Treaty that bars the spread of atomic weapons.
Iran has denied the allegations, insisting its programs are devoted only to generating electricity.
Iranian officials did not contest the finding by the IAEA inspectors but said the equipment was already contaminated by traces of enriched uranium when purchased by Tehran.
The diplomat said the report, prepared for a meeting of the U.N. agency's board, underlined the need for further inspections of the Natanz facility and Iran's nuclear programs in general to abolish concerns about the nature of its activities.
"It says that contamination is a possibility," as Iran claims, he said. "But there is work to be done to determine the plausibility of this."
Suspicion about Iran's nuclear program prompted Mohamed ElBaradei, director-general of the Vienna-based IAEA, to tour Iran's nuclear facilities in February. The visit was intended to ensure that Iran's nuclear program was limited to peaceful, civilian purposes and that the facilities were safe.
ElBaradei's tour included a visit to the incomplete nuclear plant in Natanz, about 320 miles south of Tehran. At the time, diplomats said he was taken aback by the advanced stage of a project using hundreds of centrifuges to enrich uranium.
Agency officials declined to comment on the report and what it contained. But IAEA spokesman Mark Gwozdecky said there were "a number of outstanding issues, particularly with regard to Iran's enrichment program, which require urgent resolution."
Gwozdecky said the agency's inspectors had visited Iran five times since June.
"In particular, we have visited a number of new sites, have the results of previously taken environmental samples and taken many more new samples, and are in receipt of much new information from the Iranian authorities," he said.
Analyzing the new material would take "weeks or months," he added.
In July, ElBaradei pressed Iran for "substantial progress without delay" in clarifying aspects of its nuclear program and in signing an agreement that would let U.N. inspectors conduct in-depth and comprehensive checks of Tehran's nuclear facilities.
At that time, he denied reports that agency inspectors found enriched uranium in samples taken recently in Iran, calling it "pure speculation at this stage."
Iran is building, with Russian assistance, its first nuclear reactor at Bushehr, on the shore of the Persian Gulf. It has a capacity of 1,000 megawatts and should be completed next year.
Iran's second nuclear reactor will have a capacity of 1,000 megawatts and the government is beginning feasibility studies for a 5,000 megawatt reactor, the official Islamic Republic News Agency reported earlier this month.