According to statements by Lt. Col. Anthony Shaffer and those of four others, Able Danger had identified 2 of 3 Al Qaeda cells active in the 9/11 attacks; the 'Brooklyn cell' linked to "Blind Sheik" Omar Abdel-Rahman, including September 11 attacks leader Mohamed Atta, and three of the 9/11 plot's other 19 hijackers.

In December 2006, a sixteen-month investigation by the US Senate Intelligence Committee concluded "Able Danger did not identify Mohamed Atta or any other 9/11 hijacker at any time prior to September 11, 2001", and dismissed other assertions that have fueled 9/11 Conspiracy Theories. The Senate Judiciary Committee first attempted to investigate the matter for the Senate in September 2005. The Pentagon "ordered five key witnesses not to testify", according to Senate Judiciary Committee Chairman Arlen Specter. "That looks to me as if it may be obstruction of the committee's activities", Specter, R-Pennsylvania, said at the start of his committee's hearing into the unit.

Attorney Mark Zaid, representing Lt. Colonel Anthony Shaffer and the other four Able Danger employees at the Senate Judiciary Committee hearing in September 2005, pointed out to the Committee that his clients had been forbidden by the Pentagon to testify to the Committee. He also discussed the Defense Intelligence Agency's decision to suspend Lt. Colonel Shaffer's security clearance shortly after it became known that he had provided information to the 9/11 Commission on Able Danger. "Based on years of experience I can say categorically that the basis for the revocation was questionable at best."

An investigation by the Defense Department Inspector General's office (IG) in September 2006 concluded that "the evidence did not support assertions that Able Danger identified September 11, 2001, terrorists nearly a year before the attack, that Able Danger team members were prohibited from sharing information with law enforcement authorities, or that DoD officials acted against LTC Shaffer for his disclosures regarding Able Danger." However, some of the people questioned by the IG claimed their statements to the IG were distorted by investigators in the final IG report, and the report omitted essential information that they had provided. Lt. Col Tony Shaffer has claimed that the DOD retaliated against him for speaking out publicly about the IG report's distortions.

The Senate panel of investigators said there was no evidence DoD lawyers stopped analysts from sharing findings with the FBI before the attacks. Analysts had created charts that included pictures of then-known Al Qaeda operatives, but none including Atta. A follow-up chart made after the attacks did show Atta. The Senate Committee said its findings were consistent with those of the DoD inspector general, released in September 2006.