In a heated exchange, Ms Rice had to argue with the US President in Florida not to return to the White House because it was a potential terrorist target. She told the Channel 4 documentary: "The President got on the phone and he said: 'I'm coming back'.
"I said: 'You cannot come back here. The United States of America is under attack, you have to go to safety. We don't know what is going on here'.
"He said: 'I'm coming back'. I said: 'You can't'.
"I said to him in a raised voice, and I had never raised my voice to the president before, I said: 'You cannot come back here'. I hung up.
"The president was quite annoyed with me to say the least.
"I've known the president a long time and I knew that he wanted nothing more than to be there at the helm of the ship."
Ms Rice also revealed that the bunker beneath the White House, where she was sheltering with Vice President Dick Cheney, began to run out of air.
She said: "There were so many people in the bunker that the oxygen levels started dropping and the secret service came in and said we've got to get some people out of here.
"They literally went around telling people that they weren't essential and they had to leave."
Meanwhile, the government communication systems were failing and even Mr Bush resorted to an unsecured line to talk to Washington.
Ms Rice said: "Despite all of the sophisticated hierarchy, sophisticated command and control equipment that we had, at that moment much of it didn't function very well and people instead did whatever they could to communicate messages. And frankly we then had to make it up.
"I think back on the number of cell phones that were probably used to communicate the most sensitive information because somebody was driving in or somebody couldn't get to a landline.
"And I think how really dangerous that was because if the terrorists were monitoring our communications, they would have heard a lot on cell phones."
Mr Bush gave the order authorising the airforce to shoot down any commercial airliner that was not responding.
And when United 93 came down Ms Rice and the other officials believed it may have been shot out of the sky.
She said: "Everyone in that room thinks that perhaps it's been shot down. I got on the phone with somebody at the National Military Command Centre... just saying: 'You must know whether or not you you've shot down a commercial airliner or not.'
"That was just a horrible thought that the American air force would have shot down innocent civilians, that was a horrible thought."
She continued: "As I've reflected now on what the passengers and crew of, of 93, flight 93 did, first of all there's a sense of personal gratitude that they may well have saved my life, me personally.
"I also think of what they did for the country because had another plane hit the White House or the capital I just don't think we had much more capacity to absorb greater shock than we already had."