The American military air defence command was told by the federal aviation administration that a hijacked commercial airliner was heading towards Washington 12 minutes before it hit. But during that crucial time the defence secretary, Donald Rumsfeld, and his top aides remained unaware of any imminent danger.
Defence command also failed to inform Pentagon authorities responsible for guarding the building and so no steps were taken to order an evacuation or otherwise alert the building's 20,000 employees.
During those 12 minutes two F-16 fighter jets took off in response to the threat, according to a chronology provided by the Pentagon. But they left from Virginia's Langley airforce base, 130 miles from the Pentagon, rather than Andrews air force base, which is only 15 miles away but had no planes on alert for continental air defence. Two minutes after the planes took off from Langley the Pentagon was struck by American Airlines flight 77.
There were 35 minutes between the time the second of two commercial airliners struck the World Trade Centre towers and when a third plane crashed into the Pentagon, killing 188 people including everyone on the aircraft, according to defence officials.
But while officials knew of the attacks in New York, few imagined that the Pentagon itself could be a target. Following the second attack, John Jester, chief of the defence protective service, which guards the Pentagon, raised the building's state of alert just one level, from normal to alpha, which demanded no more than spot-inspections of vehicles and increased police patrols.
Even after the Pentagon had been struck, those inside did not link the attacks they had been watching on their screens to the fire that had started to rage on the building's west side. "The first thought everyone had was that it had been a bomb," said Victoria Clarke, Mr Rumsfeld's spokeswoman.
It has also emerged that President Bush ordered US military pilots to intercept and shoot down commercial airliners over Washington if they refused to move away from the city.
"The president made the decision that if the plane would not divert, if they wouldn't pay any attention to instructions to move away from the city, as a last resort, our pilots were authorised to take them out," vice president Dick Cheney said in a televised interview.
"People say that's a horrendous decision to make, and it is," Mr Cheney said. But he added that the US "absolutely" would have acted on those orders if it could have prevented the attacks on the World Trade Centre or Pentagon.
He said the US military in effect implemented a "flying combat air patrol" over Washington. It would be up to President Bush to decide if that policy would be made permanent, Mr Cheney said.