From the New York Times :
10:32 AM : Mission Crew Commander (M.C.C.) gives the fighter pilots permission to shoot down civilian planes, an order relayed from Vice President Dick Cheney.You Can Hear The Audio At The New York Times 9/11 Tapes
Voice One : You need to read this, Region Commander has declared that we can shoot down tracks if they are not responding to our, uh, directions.
MCC Position : O.K, I’ll pass that to weapons.
Voice One : O.K.
MCC Position : The Region Com, the Region Commander has declared that we can shoot down aircraft that do not respond to our direction. Copy that? Weapons Copy that sir.
MCC Position : So if you’re trying to divert somebody and he won’t divert
Fox : D.O. is saying no.
MCC Position : No? It came over the chat. Foxy, you got a conflict on that? You got a conflict on that direction?
Fox : Right now, no, but keep checking.
Voice One : You read that from the vice president, right? The vice president has cleared —
MCC Position : Vice president has cleared us to intercept tracks.
Voice One : Of interest.
MCC Position : …And shoot them down if they do not respond, per CONR CC (Norad Continental U.S. Command Center).