The Department of Defense paid $5 per book to burn the 9,500 copies of "Operation Dark Heart," Army Reserve Lt. Col. Anthony Shaffer's memoir about going undercover in Afghanistan that the Pentagon claims revealed too many national security secrets.
A source confirmed to Fox News that while the Defense Department is making significant budget cuts, it spent in excess of $47,000 in taxpayer money to destroy the book that had earlier been cleared by the U.S. Army.
The Defense Intelligence Agency objected to the book's publication, spurring a review that resulted in its being blocked over recollections in the book about the controversial pre-Sept. 11, 2001, data mining project called "Able Danger."
Shaffer claimed in the book that Able Danger had successfully identified hijacker Mohammed Atta as a threat to the United States nearly a year before the Sept. 11 terror attacks but that information -- shared with the Sept. 11 commission after the attack -- was left out of the commission's final report.
In a letter obtained by Fox News, the DIA says national security could be breached if "Operation Dark Heart" were published in its current form.
"Apparently, Defense Intelligence Agency took exception to the way the Army cleared the book," Shaffer told Fox News in an interview conducted before he was asked by the military not to discuss the book. He confirmed efforts to block the book, a move he called "highly unusual."
However, Shaffer explained on Sunday that the distinction between the Army and DIA's rules on redaction are traced to the public domain argument. He said while the Army review found that everything he puclished is in the public domain in some form, DIA notes that much of it is still classified.
"So that's the difference in standards," he said.
A new version of the book has been published, which the book's publisher "voluntarily agreed" to do, Shaffer said.
The Pentagon is currently working with the publisher to "mitigate the resulting effects of the disclosures," a Defense Department official told Fox News
"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," the official said.
But the Pentagon's claims about national security breaches are still very much in dispute, and the Defense Department had been forced to abandon its request and a majority of others because the information was already public.
Among the information DIA objected to including in the book were references to a meeting between Shaffer and Philip Zelikow, the executive director of the Sept. 11 commission.
In that meeting, which took place in Afghanistan, Shaffer alleges he told Zelikow about "Able Danger" and Atta, the ringleader of the Sept. 11 hijackers who piloted American Airlines Flight 11 into the World Trade Center.
Shaffer, who was undercover at the time, said there was "stunned silence" at the meeting after he told Zelikow 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.
But once back in the U.S., Shaffer says he contacted the commission. Without explanation, the commission was no longer interested in his statement.
No mention of Atta's early detection was made in the final Sept. 11 commission report.
Shaffer said the Able Danger information was "clearly one of the issues" DIA had a problem with but he fought back when the Pentagon tried to strip out one paragraph since the information he included was the same as testimony he gave on Capitol Hill.
I just said, 'This is beyond the pale,'" he said, adding that other similar demands were just as "loony."
But Shaffer said the Pentagon couldn't have timed its announcement any better for Shaffer, whose book was just released and has already shot up to No. 6 on Amazon's best seller list. A check after his appearance on Fox News showed the book had reached No. 2 on Amazon.
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.
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 Awlaki for intelligence purposes after Sept. 11.
Fox News' Catherine Herridge and Jennifer Griffin contributed to this report.