Iran secured access to secret U.N. atomic agency reports almost two decades ago and circulated the documents among top officials who prepared cover stories and falsified a record to conceal suspected past work on nuclear weapons, according to Middle East intelligence officials and documents reviewed by The Wall Street Journal.

The International Atomic Energy Agency documents and accompanying Persian-language Iranian records reveal some of the tactics Tehran used with the agency, which is tasked with monitoring compliance with nuclear nonproliferation treaties and the later 2015 nuclear deal. The U.S. and the IAEA have said for years that Iran has failed to answer questions about its past nuclear work in a cat-and-mouse game that continues to this day and now complicates a revival of the nuclear deal, which lifted most international sanctions on Iran in exchange for limits on Iran’s nuclear activities.

Middle East intelligence officials said the IAEA documents, marked confidential by the agency, and Iranian records were circulated between 2004 and 2006 among senior Iranian military, government and nuclear-program officials. The agency was investigating information that suggested Iran had worked on nuclear weapons.

Iran’s acquisition of sensitive IAEA documents “represents a serious breach of IAEA internal security,” said David Albright, president of the Institute for Science and International Security and a former U.N. weapons inspector. “Iran could design answers that admit to what the IAEA already knows, give away information that it will likely discover on its own, and at the same time better hide what the IAEA does not yet know that Iran wants to keep that way.”

Iran’s Supreme Leader Ali Khamenei, speaking in Tehran on Saturday.

Photo: /Associated Press

The IAEA, based in Vienna, declined to comment on the documents and didn’t respond to questions about its handling of security.

Iranian officials didn’t respond to requests for comment. Tehran has always denied working on nuclear weapons, which Supreme Leader Ali Khamenei prohibited in a decree in 2003.

The IAEA records accessed by Iran were among more than 100,000 documents and files seized by Israeli intelligence in January 2018 from a Tehran archive. Some documents include handwritten notes in Persian on IAEA documents and attachments with Iranian commentary. In several of the documents reviewed by the Journal, Iranian officials credited “intelligence methods” for obtaining the IAEA reports.

Israel has passed the nuclear archive over to the U.S. intelligence community, said people familiar with the matter, and given partial access to independent experts, including from the Belfer Center at Harvard University. The Belfer Center concluded in April 2019 that the archive showed Iran’s nuclear work had advanced further than previously understood. The Journal reviewed documents from the archive that haven’t been disclosed publicly.

One former IAEA official said the documents from the agency are authentic, and Mr. Albright, who had access to some of the nuclear archive and wrote a book on what it revealed about Iran’s nuclear work, said the Persian-language documents reviewed by the Journal were consistent with what he had seen in other documents from the Iranian nuclear archive.

In one handwritten Persian note attached to an Iranian corporate record, a top Iranian official pressed Mohsen Fakhrizadeh, widely regarded as the father of the country’s nuclear weapons program, to come up with a “scenario” to explain to the IAEA why corporate-registration records had been changed for a civilian company that Iran claimed was working on an Iranian uranium mine.

According to a set of Iranian documents, the company, Kimiya Maadan, ceased to exist in Iranian corporate records in December 2001. One of the documents ordered Iranian officials to change Kimiya Maadan’s liquidation date in corporate records to May 2003. According to Middle East intelligence officials, the change allowed Iran to tell the IAEA that the work on the uranium mine, before May 2003, was done by Kimiya Maadan for the Atomic Energy Organization of Iran, supporting Iran’s assertion that the mine was civilian and separate from any military nuclear work.

Iran’s Ministry of Defense built the uranium mine, called Gachin, to be able to produce material for a potential nuclear-weapons program, according to Middle Eastern intelligence officials and former IAEA officials.

In Persian, the top Iranian official wrote that the IAEA was bound to ask about the accuracy of the Iranian corporate records, telling Mr. Fakhrizadeh: “We must hurry.”

In a separate instance, Iran’s intelligence service circulated on May 19, 2004, an internal IAEA report to senior officials to prepare them for an inspection—scheduled for three days later—of a heavy-water production site southwest of Tehran near the town of Arak. Tehran had told the IAEA that it planned to build a heavy-water reactor for medical and research use there. Such reactors use heavy water as a coolant and produce plutonium as a waste product, which can be used in nuclear weapons.

The IAEA document included details of satellite information and open-source evidence of Iran’s heavy-water work and a list of 18 questions the IAEA had prepared to ask Iran about its work.

An overview of the Arak heavy-water reactor facility, south of Tehran, Iran, in a file handout satellite image provided by Maxar Technologies on Jan. 8, 2020.

Photo: -/Agence France-Presse/Getty Images

Among the officials alerted about the IAEA records was

Ali Shamkhani, then defense minister and now the country’s national security chief. They were told that the IAEA had carried out an investigation of Iran’s heavy-water work.

“Photographs of 27 pages of classified documents on the following topics are being sent,” the letter said, referring to IAEA documents.

Another IAEA document obtained by Iran in 2004 was a 114-page set of reports describing uranium-conversion work that it said Iran was conducting. That process converts yellowcake into the feed material to produce enriched uranium. The file included reports on nuclear material that Iran had received from China, internal IAEA reports of the agency’s inspections of Iranian facilities and data from samples the agency had taken at Iran’s conversion facilities. It was circulated to Mr. Fakhrizadeh and one of his main deputies, Fereydoon Abbasi, as well as Iran’s defense minister and the head of its Atomic Energy Agency at the time.

Another Iranian document details steps Tehran took to keep a container with radiation-monitoring equipment out of the hands of IAEA inspectors by claiming that Iran had sold it and that there was no trace of it.

Iran also got hold of a confidential IAEA document based on Western intelligence information that included questions the IAEA wanted to ask about Iran’s so-called Green Salt project.

Green Salt was a small-scale way of producing tetrafluoride, an intermediate step in the process of producing feed material for uranium enrichment. The IAEA was concerned for years that Iran had worked on the project to give it the chance to produce nuclear fuel in a covert site, alongside any publicly declared enriched-uranium facilities.

The Journal received access to the documents from a Middle East intelligence agency that hails from a country that opposes Iran’s nuclear program.

While the U.S. and IAEA allege that Iran has been evasive about its nuclear work, the agency over time has pieced together many elements of Iran’s activities. In 2011, the IAEA published detailed information about Iran’s suspected past nuclear-weapons work, including many of the elements touched on in the documents Tehran obtained. In 2015, in a report issued as a condition of the nuclear deal, the IAEA concluded that Iran had a “coordinated effort” in place to work on nuclear weapons until at least 2003.

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Iran’s alleged stonewalling of the IAEA’s investigations continues to cast a shadow over the Biden administration and European countries’ efforts to revive the 2015 Iranian nuclear deal, which the Trump administration left in 2018. Talks have stalled in recent weeks on reviving the pact.

Iran wants the IAEA’s continuing investigations into its past nuclear-weapons work closed before a deal is restored. The IAEA and Iran agreed to intensive talks this spring with an aspiration for the agency to have enough clarity on Iran’s nuclear work that the IAEA board of member states could close the investigation in June. But Iran has continued to stall the probe, IAEA officials said.

“Iran, for the time being, has not been forthcoming in the kind of information we need from them,” IAEA Director General Rafael Grossi said to the European Parliament earlier this month.

One former George W. Bush administration official who worked on Iran issues said Washington officials had long suspected that Tehran was seeking access to IAEA documents at the time but there was never any proof.

“There was substantial concern about Iran penetrating the IAEA and using the material it acquired to misdirect the inspections and hide its violations of the Safeguards Agreement,” said the official.

Corrections & Amplifications
Ali Shamkhani was Iran’s defense minister. An earlier version of this article incorrectly described him as the head of Iran’s armed forces. (Corrected on May 25)

—Michael R. Gordon contributed to this article.

Write to Laurence Norman at laurence.norman@wsj.com and Sune Engel Rasmussen at sune.rasmussen@wsj.com