The Iranian government, which is known neither for transparency nor candor, has insisted for many years that the goal of its nuclear program is entirely peaceful. And for many years, the International Atomic Energy Agency, whose motto is “Atoms for Peace,” has tended to give the ayatollahs the benefit of the doubt on this question.

The agency’s former chairman, Mohamed ElBaradei, now a candidate for the presidency of Egypt, seemed to take the attitude that anxiety about Iran’s nuclear objectives was motivated by the strategic self-interest, even the paranoia, of the U.S., Israel and the Arab states near Iran, rather than by the reality-based worry that bloody-minded mullahs bent on dominating the Middle East aren’t the sort of people who should have the bomb.

The new chairman of the IAEA, Yukiya Amano of Japan, seems more skeptical of Iran’s claim of nuclear virginity. He is, by many accounts, preparing a comprehensive indictment of Iran’s nuclear program to be issued later this year. As an interim step, his agency recently issued a report on Iran’s nuclear activities that might help concentrate the attention of a world that has lately been preoccupied by the revolutions in Libya, Yemen and Syria.

These are important events, but an Iran with a bomb? This would bring about a nuclear arms race in the world’s most volatile region. It would pose a serious threat to the smooth flow of oil out of the Persian Gulf. And it would mean the end of American influence in the Middle East. Not to mention the potential for an actual nuclear exchange between Israel and Iran.

IAEA’s New Report

The IAEA’s new report makes for dry reading -- the agency doesn’t turn out propulsive narratives -- but strongly suggests that the mullahs haven’t gone into the nuclear business because of their keen interest in clean energy. Using information gathered from member states’ intelligence agencies, it cites seven possible “undisclosed nuclear related activities” on the part of Iranian nuclear scientists. These include experiments to build atomic triggers, studies of the type of instruments needed for testing explosives underground, and the development -- this is a mouthful -- “of explosive components suitable for the initiation of high explosives in a converging spherical geometry.”

Iran’s nuclear scientists might be building atomic triggers as a weekend hobby, and they might have discovered a sports-related reason to initiate explosives in a converging spherical geometry. But if the IAEA’s suspicions prove correct, then Iran is actively trying to make a nuclear warhead.

Pattern of Deception

“The IAEA is certainly worried that Iran has an ongoing program to develop and build nuclear weapons components,” David Albright, a former IAEA inspector who now heads the Institute for Science and International Security, told me. Albright, along with many other experts, discerns a pattern of deception in Iran’s behavior, exemplified by the regime’s decision to build a secret uranium-enrichment facility deep inside a mountain near Qom, the existence of which was exposed by Western intelligence agencies in 2009.

A peaceful, internationally supervised nuclear program presumably would have no need for secret uranium-enrichment facilities buried inside mountains.

News about possible advances in weapons design wouldn’t be so dire if Iran was still having trouble making nuclear fuel. Last year, the Stuxnet virus -- the only computer virus about which anyone has ever said anything nice -- was thought to have crippled a substantial number of Iran’s centrifuges. The virus, apparently a joint project of Israel, the U.S. and several European countries, was the most overt sign that a sophisticated international program of subterfuge and sabotage directed against Iran’s nuclear program was doing real damage.

Growing Enrichment Capacity

Stuxnet now appears to have been a more perishable virus than previously thought. Signs are abundant that Iran is accelerating its manufacture of low-enriched uranium, the necessary precursor to highly enriched uranium. The Federation of American Scientists reported in January that “calculations using IAEA data show that the enrichment capacity at Iran’s commercial-scale enrichment facility at Natanz has grown during 2010 relative to previous years. The boost in capacity is due to an apparent increase in centrifuge performance.”

This latest IAEA report buttresses the federation’s finding, noting that inspectors who had recently visited the Natanz facility now believe Iran is producing low-enriched uranium at a faster pace than before the centrifuges were hit by Stuxnet. Various Western intelligence agencies and independent analysts think that the Iranians already possess enough low-enriched uranium to produce two or three bombs.

Khamenei’s Options

What all this means is that the IAEA is deeply worried that the Iranians are approaching a moment of decision -- the point at which the country’s nuclear scientists could tell Ayatollah Ali Khamenei, Iran’s supreme leader, that they’re ready to make him a bomb for testing.

Khamenei would then face three options. He could shelve the program for a later day. He could order a nuclear break-out, in which Iran expels the IAEA inspectors and enriches its uranium to bomb-grade levels. Or he could try what is known as a sneak-out, in which his scientists create bomb-grade uranium in a secret facility.

The chance that he would choose the break-out option is small. It would take Iran anywhere from six months to a year after expelling the inspectors to enrich uranium to bomb strength, and in this period it’s almost guaranteed that Israel or the U.S. would bomb its nuclear facilities. (I believe firmly, after two years of reporting on the Iranian nuclear program, that President Barack Obama would order air strikes if he thought Iran was moving definitively to become a nuclear-armed state).

Sneak-out, then, would be the more attractive option -- which is why intelligence agencies across the globe are searching relentlessly for a “son of Qom,” an as-yet-undiscovered nuclear facility similar to the one found at Qom.

Intelligence Limitations

There will always be those who doubt that Iran seeks to be a nuclear-armed state. And these doubts are useful: Iraq has taught many of us important lessons about the limitations of intelligence. But we’ve also learned a different lesson recently from Syria. Last month, at the same time it was airing its suspicions about Iran, the IAEA issued another report, in which it found that Syria was “very likely” operating a clandestine nuclear program until 2007, when Israel bombed what was allegedly a secret Syrian reactor. Shortly after the attack, Seymour Hersh, in an article skeptical about such claims, quoted ElBaradei, then the head of the IAEA, as saying, “Our experts who have carefully analyzed the satellite imagery say it is unlikely that this building was a nuclear facility.”

The most important mission of the IAEA -- and one of the most important missions of the Obama administration -- is to know all that it is possible to know about Iran’s intentions, and to subvert these intentions in all possible ways. Because it will be a very bad day indeed when it is an underground nuclear test that informs us of Iran’s intentions.

(Jeffrey Goldberg is a Bloomberg View columnist. The opinions expressed are his own.)

To contact the author of this column: Jeffrey Goldberg at goldberg.atlantic@gmail.com.

To contact the editor responsible for this column: Timothy Lavin at tlavin1@bloomberg.net.