No public inquiry in American history has gone as far in scraping away the layers of official secrecy and laying bare the machinery of government.

In doing that, the September 11 commission has revealed not the mighty apparatus of popular imagination but a dysfunctional contraption incapable of protecting the country against its most immediate and deadly threat.

Only the Warren commission into President Kennedy’s assassination came close in gripping the public’s attention, but the September 11 investigation has cut deeper, unearthing and publishing secret documents initially intended for the president alone, while offering glimpses of the CIA’s most clandestine operations.

The conclusions were unveiled yesterday in a hall of Greek columns and ornate gilt decor, along Washington’s sweeping National Mall, a scene befitting the world’s sole superpower.

But the report peered behind the facade and showed the decay and complacency of a country which assumed itself so invulnerable that it ignored a string of “blinking red” signs.

Coming at a time when evidence is emerging daily that a combination of a blinkered, ideological administration and incompetent intelligence analysis took the US and its allies into a war in Iraq on baseless justifications, yesterday’s report could trigger a crisis of faith in America’s most powerful institutions.

The CIA, usually portrayed as ruthless and omniscient, turns out to have had no spies and barely any informers in the enemy camp. Against al-Qaida, it was virtually blind and its leaders were paralysed by caution. When it did chance on two of the plotters and put them under surveillance in Malaysia in 2000, it almost immediately lost track of them.

The FBI, another supposed pillar of power, had sharp and dedicated agents around the country but their warnings were ignored by time-servers in Washington.

The bureau’s computers were ancient and a barrier to the sharing of information.

The Norad military command, primed to defend against nuclear missiles, had not taken seriously the possibility that a commercial plane could be turned into a missile by hijackers.

The immigration service  so vigilant in barring some migrant workers from entry  failed to spot the hijackers’ bogus passports, questionable cover stories and false statements on their visa application forms. Worst of all, the report presented a picture of a country failed by two administrations.

The Clinton White House grew anxious about the threat of a catastrophic attack, but was too risk-averse politically to convert its worst fears into action.

It was followed by an administration dismissive of threats that did not fit its preconceptions and thought it had years to confront al-Qaida.

It is hardly surprising the Bush White House never wanted the commission.

When it was forced into it, largely by the overwhelming moral pressure imposed by the victims’ families, the administration opted for the next best thing to no inquiry: one chaired by Henry Kissinger, a lifelong champion of executive privilege.

After a fortnight as chairman, however, Mr Kissinger decided his consultancy contracts were too valuable to surrender under conflict of interest rules and stepped down in December 2002.

His successor, Thomas Kean, a Republican has not proved the party man the administration expected.

Mr Kean publicly confronted the White House over its failure to hand over classified documents. He also refused to allow Vice-President Dick Cheney to bully the commission out of its conclusion that there was no serious evidence of collaboration between Saddam Hussein and al-Qaida.

Inevitably in an election year, the report avoids making definitive judgments about the administration that might easily be cut-and-pasted into a John Kerry political advertisement.

A definitive judgment that the September 11 attacks should have been prevented could have been devastating to President Bush in November, and it would have dropped the report into the political shouting match along with all the other election year books.

The commission avoided that, but its report and the more bluntly worded staff statements that preceded it have put enough secret information into the public arena for anyone to come to their own conclusion.

The report makes the point repeatedly that the al-Qaida hijackers were not infallible, and it presents a litany of missed opportunities to stop them.

“Since the plotters were flexible and resourceful, we cannot know whether any single step or series of steps would have defeated them,” the commission concluded. “What we can say with confi dence is that none of the measures adopted by the US government from 1998 to 2001 disturbed or even delayed the progress of the al-Qaida plot.”

There is unlikely to be much argument about that. But the commission’s recommendations are not necessarily shared by those in the intelligence and security worlds who are most critical of the status quo.

They argue the immediate priorities are practical: more spies need to be recruited, trained and infiltrated, the FBI needs to buy some decent computers and more money needs to be spent on monitoring the millions of shipping containers that enter the US every year.

They do not believe that America can afford the time for a bureaucratic reorganisation.

The conclusions of the Butler report provoked skepticism among former US intelligence officials yesterday, who variously described it as gentlemanly, shallow and clubbish.

Most described Lord Butler’s conclusions as politically driven, and compared them to last week’s parallel report by the Senate intelligence committee, which similarly found the White House was not to blame for the Iraqi intelligence fiasco. However, the Senate committee lambasted the CIA’s leadership, while the Butler report was less brutal about MI6. Vincent Cannistraro, a former CIA chief of operations for counter-terrorism, said: “I can tell you there’s rampant jealously in the CIA, where they wish they could have had a report more like Butler’s. It was much more nuanced, much more fair.”

The familiar paraphernalia of political scandal are being assembled in Washington. At the last count, two criminal inquiries and six congressional hearings were scheduled on the Enron matter. In the legislature, reduced by the war on terrorism to the role of cheerleader, everyone wants to be a part of it. Both parties know how the rituals of scandal can define a presidency. President Reagan managed to shrug off most of the damage caused by the Iran-Contra affair, while President Clinton was overwhelmed by the Monica Lewinsky saga and is unlikely to have an airport named after him.