Said Bahaji, a German citizen, was a close friend of Mohammed Atta, the hijacker in control of American Airlines Flight 11 which was the first plane to strike the World Trade Center.
Terrorism analysts say he was an important member of the Hamburg cell that plotted the attacks, which included Attah and the other hijackers. The passport indicates he left Germany for Pakistan about one month before the attacks 9/11 attacks on Aug. 3, 2001.
"This could mean he's been contributing to al Qaeda ever since he went to Afghanistan-Pakistan border before 9/11," said Richard Clarke, an ABC News Consultant and former White House terrorism czar who wrote the 9/11 Commission Report.
Bahaji's passport was found in the volatile region of South Waziristan in Pakistan.
Terrorism analysts who have suspected he joined al Qaeda in Pakistan say he must have moved up the ranks in al Qaeda during the previous nine years, if he is still alive.
"The big question is if he is dead or not," said Guido Steinberg, a Berlin based terror analyst and expert on the 9-11 Hamburg cell.
German authorities charged Bahaji with 3,000 murders, but have been unable to track him in Pakistan.
In 2003, he sent a package to his wife who still lives in northern Germany, according to Steinberg. Other than that one correspondence, Steinberg says authorities in Berlin have not had any more information about his whereabouts.
ABC News obtained a video from Bahaji's wedding at a mosque in Hamburg from October 1999 where a smiling Bahaji greets relatives and friends, including other members of the Hamburg cell.
He lived for almost a year with Atta between November 1998 and July 1999, as the hijack plans were being finalized.
Other members of the Hamburg cell include Ziad Jarrah, pilot of United 93, Marwan al-Shehhi, pilot of United 175 which crashed into the second World Trade Center, and Ramzi Binalshibh, who failed to obtain a U.S. Visa and therefore acted as a go-between for Atta, Jarrah, al-Shehhi and the other hijackers, passing on information from key al-Qaeda figures regarding details such as targets and wire transfers.
Bahaji is son of a Moroccan immigrant, and was the only German citizen in the Hamburg cell. Educated in Morocco, he returned to Germany to study electrical engineering at the Technical University of Hamburg-Harburg.
Bahaji spent five months in the German army before obtaining a medical discharge.
The 9-11 Commission Report described him as an "insecure follower with no personality and with limited knowledge of Islam," but said that he "nonetheless professed his readiness to engage in violence."
A passport belonging to Raquel Gacia Burgos, the Spanish wife of a senior al-Qaeda operative, was also found, the Pakistan army said. Burgos, who Spanish media report has not been seen by her family in Madrid since 2001, is the wife of Amer Azizi, a Moroccan sought for his suspected role in the March 2004 attacks on commuter trains in Madrid.
Azizi has been linked by Spanish investigators to members of the group that carried out the Madrid attacks and is considered to be one of al-Qaeda's leaders in Europe.
The U.S. State Department did not immediately respond to ABC News' request for comment on this story.