The discovery was made by a Pentagon intelligence unit,Able Danger, set up in 1999 by the military's Special Operations Command to gather information about al-Qa'ida around the world.
The team identified a so-called Brooklyn Cell affiliated to the terrorist group. Apart from Atta, it included Marwan al-Shehhi, as well as Khalid al-Mihdhar and Nawaf al-Hazmi - the two 19 hijackers who had also been identified by the CIA as potential threats in mid-2000, but whose names the intelligence agency did not pass on to the FBI until months before the attacks.
Details were first given in June by Curt Weldon, a Republican Congressman specialising in intelligence and security, but attracted little notice at the time. Yesterday, however, they appeared on the front page of The New York Times, which quoted not only Mr Weldon but an unidentified former defence intelligence official with knowledge of the Able Danger operation. By summer 2000, the former official said the special unit had put together a massive chart showing known al-Qa'ida networks around the world. It included the names and photographs of Brooklyn Cell members.
Able Danger recommended that the information be passed on to the FBI. This was turned down because the four either had green cards allowing permanent residence, or valid entry visas. No less astonishing, details do not appear to have been passed on to the bipartisan 9/11 Commission set up by George Bush in 2003. It was told about the existence of Able Danger - but not that Able Danger had identified Mr Atta and three colleagues.
Yesterday, Donald Rumsfeld, the Defence Secretary, flatly refused to comment on the affair.