When it comes to politicized intelligence in the Bush years, the critics may finally have a point. Perhaps the work of America’s intelligence agencies was manipulated to suit the convenience of a small group of willful officials, intent on getting their way against the better judgment of their colleagues.

Except the intelligence was about Iran, not Iraq, and the manipulators weren’t conniving neocons but rather the Administration’s internal critics on the left.

That’s one way to look at last month’s revelation that Iran is building a secret second site to enrich uranium, among other emerging intelligence details. The Qom site—too small for civilian purposes but ideal for producing weapons-grade uranium—is supervised by Iran’s Revolutionary Guards and was only declared to the International Atomic Energy Agency after Tehran got wind that the nuclear watchdogs knew about it.

But the more telling detail, as a recent White House “guidance paper” acknowledges, is that the U.S. has been “carefully observing and analyzing this facility for several years.” That timeline is significant, because it was less than two years ago, in December 2007, that a National Intelligence Estimate on Iran’s nuclear programs asserted with “high confidence” that Tehran had “halted its nuclear weapons program” in the fall of 2003.

The NIE was a political sensation, seized on by Democrats and Iraq war critics as another case in which the Bush Administration had supposedly politicized intelligence. Iranian President Mahmoud Ahmadinejad called the NIE a “declaration of victory,” and it derailed any hopes for the Bush Administration to garner international support for tougher sanctions on Iran.

Yet some of us noted at the time that the NIE added, in a crucial footnote, that by “nuclear weapons program” it meant “weapon design and weaponization work and . . . uranium enrichment-related work,” rather than Iran’s “declared” nuclear facilities. The NIE’s main authors—including former intelligence official Tom Fingar and other internal critics of Bush Administration policies—downplayed this critical detail. Never mind that it was precisely Iran’s “declared” nuclear facilities that constituted the core element of any nuclear-weapons program.

Fast forward to the present, and it turns out the NIE was misleading even on its own terms: Iran did have a covert facility, perhaps for enrichment, and the intelligence community knew or at least strongly suspected it. We are also learning that the NIE’s judgment puts the U.S. intelligence community at odds with its counterparts in Britain, Germany and Israel, which have evidence to show that Iran resumed its weaponization work after 2003.

The Wall Street Journal Europe reported on July 30 that Germany’s foreign intelligence agency, the BND, “has amassed evidence of a sophisticated Iranian nuclear weapons program that continued beyond 2003. This usually classified information comes courtesy of Germany’s highest state-security court. In a 30-page legal opinion on March 26 and a May 27 press release in a case about possible illegal trading with Iran, a special national security panel of the Federal Supreme Court in Karlsruhe cites from a May 2008 BND report, saying the agency ‘showed comprehensively’ that ‘development work on nuclear weapons can be observed in Iran even after 2003.'”

The 2007 NIE also contradicts the findings of the usually hypercautious IAEA, which concluded in a recent analysis that Iran “has sufficient information to be able to design and produce a workable implosion nuclear device.” The word “implosion” is especially significant because it means Iran is likely seeking to design a warhead compact enough to be fitted atop one of its increasingly capable ballistic missiles.

It’s of course possible that the U.S. has it right and everyone else has it wrong. But given the stakes if Iran does get the bomb, and given everything we know about Iran’s history of deception, the obligation of intelligence agencies is not to issue politically skewed “estimates” that derail U.S. policy to stop the Iranian program. Getting it wrong on Iran—the most crucial intelligence question of the decade—would be no small footnote in the CIA’s history of intelligence blunders.