Intelligence estimates about foreign nuclear programs seem to lead unhappy, often controversial, lives.

There was the 2002 National Intelligence Estimate that Iraq had reconstituted its nuclear weapons program. That was wrong, of course. But there is a body of thought, built up on the American left, that the estimate was beyond wrong. It holds that there was a conspiracy to cook the intelligence to support a preconceived course of action; that the Bush administration, especially the vice president, pressured intelligence workers to reach the conclusions they did. “Bush lied, Americans died” was the commonly heard mantra.

In fact, we just got it wrong. In one of my last meetings with Leon Panetta when he was taking over as director of the CIA, I cautioned against accepting the left’s urban legend and said, “Leon, this was our fault. It was a clean swing and a miss.”

Five years later, it was the American right that attacked an intelligence estimate, this one about Iran and its nuclear program. I heard one of its opponents describe this estimate as “morally corrupt,” claiming that it was a sort of revenge by the intelligence community for the controversy over its Iraq judgments.

In fact, in the summer of 2007, U.S. intelligence analysts were working to update an aging assessment on Iran. That older assessment held that Iran was “determined” to acquire a nuclear weapon, and we were preparing to publish an update that reaffirmed that conclusion, though we were also going to downgrade the confidence level from high to medium — not because we had information to the contrary but simply because the confirmatory information was aging and we had little fresh data to support it.

That summer, however, new data began to accumulate. The information suggested that Iran had stopped the weaponization of fissile material, work that would be required to design a reliable warhead. The more difficult tasks — creating fissile material and developing missile delivery systems — continued unabated, but there appeared to be good evidence that this one aspect had largely been put on the shelf.

None of us was blind to the reality that this conclusion would make it more difficult for the United States to isolate Iran and build an international consensus against its nuclear program. We also knew that we could be wrong. But this is where the data were taking us, and the Bush administration, to its credit, directed that we make our findings public. We did, with predictable results.

Today we are engaged in controversy over a third estimate, this one dealing with the nuclear reactor at al-Kibar, in eastern Syria. The debate has been stoked by former vice president Dick Cheney’s memoir and some follow-up articles.

Writing in The Post last week, Bob Woodward described my assessment given at a meeting in the White House residence during the summer of 2007: “That’s a reactor. I have high confidence. That Syria and North Korea have been cooperating for 10 years on a nuclear reactor program, I have high confidence. North Korea built that reactor? I have medium confidence. On [the question whether] it is part of a nuclear weapons program, I have low confidence.”

To be clear about the last point: I told the president that al-Kibar was part of a nuclear weapons program. Why else would the Syrians take such a risk if they were not gambling on such a game-changer? And, besides, we could conceive of no alternative uses for the facility. But since we could not identify the other essentials of a weapons program (a reprocessing plant, work on a warhead, etc.), we cautiously characterized this finding as “low confidence.”

Woodward describes the intelligence as fact-based but then says it was shaped to discourage a preemptive U.S. strike.

That’s not what intelligence does, and confusion on that point may have been generated by a coin, mentioned by Woodward, that CIA folks working on al-Kibar made after the facility was destroyed. On that coin, emblazoned across a map of Syria, were the four words that had been the rallying cry of this effort: “No core, no war.”

Except that “no war” was never taken to mean no kinetic option against al-Kibar. Rather, it referred to the overall policy direction we were following: Whatever we did to make this reactor go away (“no core”), it could not lead to a generalized conflict in the Eastern Mediterranean (“no war”).

Hence, knowledge of the facility was closely held within the U.S. government. Congressional notifications were limited. Even within the executive branch, the data were compartmentalized. All of this was designed to prevent a leak and preclude a circumstance in which we put Syrian President Bashar al-Assad in a position where he felt publicly humiliated and thought he had to respond if the facility were attacked.

As it happened, the plutonium plant at al-Kibar was destroyed by the Israelis in September 2007. Neither the Syrian, U.S. nor Israeli governments said much about it. Assad let the facility’s destruction pass. “No core, no war.”

It’s puzzling to me why al-Kibar has been resurrected. We were wrong about Iraq’s nuclear program. Fair enough. History will tell how right or wrong we were about Iran. I can accept that.

But we got al-Kibar right. And the debate in the U.S. government over its fate was informed by hard facts. The debate reflected differing views, differing approaches. They were aired. Decisions were made. Isn’t that how it’s supposed to work?

The writer was director of the CIA from 2006 to 2009.