That Iran is building a secret underground facility near the holy city of Qom, under custody of the Revolutionary Guard—too small to be a production center for nuclear fuel, but just right for the enrichment of uranium to weapons grade—is grounds for concern, but not panic.

Heretofore, all of Iran’s nuclear facilities, even the enrichment plant at Natanz—kept secret before exiles blew the whistle in 2002—have been consistent with a peaceful nuclear program.

Iran has also been on solid ground in claiming that, as signatory to the Non-Proliferation Treaty, she has a right to enrich uranium and operate nuclear plants, as long as she complies with treaty obligations.

Under the Safeguard Agreement to the NPT, these include notification, six months before a nuclear facility goes operational.

According to U.S. officials, construction of this site began in 2006 and is only months from completion. And Tehran did not report it to the International Atomic Energy Agency until a week ago, when they were tipped the Americans were onto it and about to go public.

Iran’s explanation: This facility is benign, a backup to Natanz, to enable Iran to continue enriching uranium to fuel grade, should America or Israel bomb Natanz. It is a hedge against attack. And contrary to what Barack Obama implies, the facility is designed to enrich uranium only to the 5 percent needed for nuclear fuel, not the 90 percent needed for nuclear weapons.

Still, the burden of proof is now upon Tehran.

President Ahmadinejad and Ayatollah Khamenei must convince IAEA inspectors this small secret facility that can house only 3,000 centrifuges has the same purpose as Natanz, which can house 58,000. Or they will be exposed as liars—to the West, to the Russians who have served as their defense counsel and to their own people.

For while Iranians are near unanimous in backing their national right to peaceful nuclear power, they do not all want nuclear weapons. And the Ayatollah has declared, ex cathedra, that Iran is not seeking them, and possession or use of such weapons is immoral and contrary to the teachings of Islam.

If Obama is right that the secret facility is “inconsistent with a peaceful program,” but compatible with a weapons program, Ayatollah Khamenei has a credibility problem the size of Andrei Gromyko’s, when he assured President Kennedy there were no Soviet missiles in Cuba. And President Kennedy had the photos in his desk.

Diplomats have been called honest men sent abroad to lie for their country. But ayatollahs, as holy men, are not supposed to be descending to diplomatic duplicity.

Obama’s dramatic announcement represents a coup for U.S. intelligence, but it also raises questions.

Reportedly, we have known of this Qom facility “for several years.” Yet, in late 2007, the National Intelligence Estimate (NIE) said that U.S. agencies had “moderate confidence” that Iran had ended any nuclear weapons program in 2003.

In August, Walter Pincus, in a Washington Post story—“Iran Years From Fuel for Bomb, Report Says”—wrote, “Despite Iran’s progress since 2007 toward producing enriched uranium, the State Department intelligence analysts continue to think that Tehran will not be able to produce weapons-grade material before 2013.”

This was the judgment of the State Department Bureau of Intelligence and Research, based on “Iran’s technical capability.”

Query: If State’s top intelligence analysts, this year, did not think Iran could enrich to weapons grade until 2013, had they been kept in the dark about the secret facility near Qom?

Two weeks ago, in a Web exclusive, Mark Hosenball wrote, “The U.S. intelligence community is reporting to the White House that Iran has not restarted its nuclear weapons development program, two counter-proliferation officials tell Newsweek.”

The officials told the White House the conclusion of the 2007 NIE—i.e., Iran had halted its weapons program in 2003—stood.

Were these two counter-proliferation officials also out of the loop on the secret site? Or did they know of it, but fail to share the sense of alarm and urgency President Obama showed last week?

Despite last week’s revelation, the Obama policy of talking to Tehran makes sense. Whatever the ayatollah’s intentions, IAEA inspectors have his lone ton of low-enriched uranium at Natanz under observation. To enrich it to weapons grade, it must be moved.

America’s twin goals here are correct, compatible and by no means unattainable: no nukes in Iran, no war with Iran.

Bombing would unite that divided country behind a regime whose repressed people detest far more than we, as they have to live under it. Patience and perseverance, as in the Cold War, may be rewarded with the disintegration of a state that is today divided against itself.

We outlasted the Red czars. We will outlast the ayatollahs.