The audio files and transcripts appear on the Rutgers Law Review website and were first reported on Thursday by The New York Times.
The discussion topics begin with early reports of hijackings and include the scrambling of fighter jets.
In one excerpt, someone in a New York radar control center says: "Another one just hit the building."
Someone responds: "Oh my God."
And then: "Another one just hit it hard. ... Another one just hit the World Trade."
It's followed by: "The whole building just, ah, came apart."
Someone utters again: "Oh my God."
The audio compilation was made as part of the 9/11 Commission investigation into al-Qaida's attacks, but was not completed before the commission shut down in 2004. Much of the audio and its transcripts have been made public before in hearings, lawsuits and various government reports.
The dean of the Rutgers Law School, John Farmer, was a lawyer for the 9/11 Commission and published many of the transcripts in his 2009 book, "The Ground Truth." Farmer and Rutgers law school students helped finish reviewing and transcribing the final files.
The recordings show the confusion that reigned among military commanders and air traffic controllers after the hijackers turned off their aircraft transponders, making it difficult for radar to track them.
The military learned about the hijacking of American 11 nine minutes before it crashed into the World Trade Center, and was never notified about the other hijackings before those planes crashed.