The Pentagon has burned 9,500 copies of Army Reserve Lt. Col. Anthony Shaffer's memoir "Operation Dark Heart," his book about going undercover in Afghanistan.

A Department of Defense official tells Fox News that the department purchased copies of the first printing because they contained information which could cause damage to national security.

The U.S. Army originally cleared the book for release.

The U.S. Defense Intelligence Agency attempted to block the book about the tipping point in Afghanistan and a controversial pre-9/11 data mining project called "Able Danger."

In a letter obtained by Fox News, the DIA says national security could be breached if "Operation Dark Heart" is published in its current form. The agency also attempted to block key portions of the book that claim "Able Danger" successfully identified hijacker Mohammed Atta as a threat to the United States before the Sept. 11, 2001, terror attacks.

Click here to read the full DIA letter (pdf)

Specifically, the DIA wanted references to a meeting between Lt. Col. Tony Shaffer, the book's author, and the executive director of the 9/11 Commission, Philip Zelikow, removed. In that meeting, which took place in Afghanistan, Shaffer alleges the commission was told about "Able Danger" and the identification of Atta before the attacks. No mention of this was made in the final 9/11 report.

Shaffer, who was undercover at the time, said there was "stunned silence" at the meeting after he told the executive director of the commission and others that Atta was identified as early as 2000 by "Able Danger."

"Dr. Philip Zelikow approached me in the corner of the room. 'What you said today is very important. I need you to get in touch with me as soon as you return from your deployment here in Afghanistan'," Shaffer said.

Once back in the U.S., Shaffer says he contacted the commission. Without explanation, the commission was no longer interested. An inspector general report by the Department of Defense concluded there was no evidence to support the claims of Shaffer and others. But Fox News has obtained an unredacted copy of the IG report containing the names of witnesses, who backed up Shaffer's story when contacted for comment.

Atta was the alleged ringleader of the Sept. 11 hijackers and piloted American Airlines Flight 11 into the World Trade Center.

Shaffer spoke to Fox News before he was asked by the military not to discuss the book. He confirmed efforts to block the book and other details.

Calling the move "highly unusual," he explained that the book had already been cleared for release when the DIA stepped in.

"Apparently, Defense Intelligence Agency took exception to the way the Army cleared the book," he told Fox News.

The DOD says Shaffer and the book’s publisher ‘voluntarily agreed’ to remove what it deemed to be classified information prior to the book’s first printing.

“Given the sensitive nature of this request and the potential damage to national security, the Department of Defense had every reason to believe that this would be handled with the utmost discretion by all of the parties. Unfortunately, someone disclosed to the press these ongoing efforts before the Department of Defense had the opportunity to finish working with the publisher on a corrected version,” a DOD official told Fox News.

The DOD is currently working with the publisher to ‘mitigate the resulting effects of the disclosures,’ the official said.

The documents and exclusive interviews, including an Army data collector on the Able Danger Project, are part of an ongoing investigation by the documentary unit "Fox News Reporting" which uncovered new details about American cleric Anwar al-Awlaki and efforts by the FBI to track and recruit him for intelligence purposes after 9/11.

Fox News' Catherine Herridge and Jennifer Griffin contributed to this report.