Iran’s production of nuclear fuel plunged in recent weeks, the United Nations atomic agency reported on Monday, following alleged sabotage of its main nuclear facility in April that Tehran has blamed on Israel.

The drop in production, detailed in the International Atomic Energy Agency’s confidential report circulated Monday, gives the first substantive insight into the impact of the incident, which took out the power supply at Natanz and destroyed potentially hundreds of centrifuges, machines that enrich uranium.

Israel has declined to comment on the incident, one of several at Iran’s nuclear facilities over the last 18 months. Tehran accused Israel at the time of orchestrating the attack to undermine the start of talks in Vienna involving Iran and the U.S. aimed at restoring the 2015 nuclear deal. Former President Donald Trump withdrew the U.S. from the deal in 2018.

Iran’s stockpile of enriched uranium increased by an estimated 273 kilograms in the three months ending May 22, the IAEA said, just over half the 525 kg stockpile increase in the previous quarter. The Natanz incident happened April 11, halfway through the reporting period.

The agency also reported that on May 24, there were 20 cascades of centrifuges working at the fuel enrichment plant at Natanz, a sharp decrease from before the April incident.

Iran’s total stockpile is now estimated to be around 3,241 kilograms, about 16 times higher than the permitted stockpile in the 2015 agreement. Experts say that amount is likely enough nuclear material, if purified to weapons-grade level, for up to three nuclear weapons.

Iran responded to the Natanz incident by starting to produce uranium enriched to 60% for the first time, a level close to weapons grade, and by saying it would install more advanced centrifuges at the site.

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In its report, the IAEA said Iran had only produced 2.4 kilograms of 60% enriched uranium. Its stockpile of 20% enriched uranium reached 63 kilograms. The rest is low-enriched material.

At the time of the Natanz incident, Iran played down the damage done. Ali Akbar Salehi, the head of Iran’s atomic agency, said the country’s enriched- uranium production was progressing vigorously. Iran also introduced more advanced centrifuges, which would increase its production speed.

Some Israeli and Western officials have said, however, that the incident may have made a serious dent in Iran’s medium-term production, potentially keeping Iran’s enrichment capabilities at lower levels through much of this year. There are doubts about the efficiency of the machines Iran is using to replace the damaged centrifuges.

Last week, IAEA Director General Rafael Grossi called Iran’s broadening nuclear program “very concerning,” saying only countries producing nuclear weapons were enriching uranium to 60% levels.

Biden administration officials have said Iran’s advancing nuclear program underscores the need to restore the 2015 deal, which placed strict but temporary restrictions on Iran’s nuclear activities.

Iran lifted its uranium stockpile above the 2015 deal’s permitted levels in July 2019, responding belatedly to the Trump administration’s decision to quit the agreement and impose economic sanctions on Tehran.

Western officials say Iran’s nuclear buildup has been designed to pressure the Biden administration into lifting sanctions and restoring the 2015 deal on Iran’s terms. President Biden has set a return to the agreement as a foreign- policy goal.

Talks started in April on a path for the U.S. and Iran to return to the agreement. The discussions have dragged on past the mid-May target deadline with no agreement yet on which sanctions the U.S. would keep in place and what steps Tehran would take to strip back its nuclear program.

On Monday, Iran’s chief negotiator at the talks, Abbas Araghchi, said the parties, which include the U.S., Iran, Russia, Britain, France and Germany, could take a break from talks soon to consult in capitals, a view echoed by senior Western diplomats.

Concerns are growing that with less than three weeks to go before Iran’s presidential elections, the talks could soon go on hold.

In a separate report issued Monday, the IAEA criticized Iran’s lack of cooperation in explaining the agency’s discovery of undeclared nuclear material at several locations in Iran since the fall of 2019.

The issue could lead to fresh tensions between Iran and the agency even if the nuclear deal is restored. Critics of the deal say the undeclared material is part of a range of evidence suggesting Iran didn’t close off its nuclear-weapons options and has maintained material, documents and equipment generated from past work.

The agency said Iran had failed to produce any real answers backed up by documents to answer any of the questions in its probe.

Iran’s ambassador to the IAEA said Monday evening on Twitter that Iran had “done its utmost” to cooperate with the agency and hoped the probe could be concluded as soon as possible.

“The lack of progress in clarifying the Agency’s questions…seriously affects the ability of the Agency to provide assurance of the peaceful nature of Iran’s nuclear program,” the agency said in its report.

Write to Laurence Norman at laurence.norman@wsj.com