In a statement to CNN, Cunningham said defense officials observed the September 20 destruction of about 9,500 copies of Army Reserve Lt. Col. Anthony Shaffer's new memoir "Operation Dark Heart."
Shaffer says he was notified Friday about the Pentagon's purchase.
"The whole premise smacks of retaliation," Shaffer told CNN on Saturday. "Someone buying 10,000 books to suppress a story in this digital age is ludicrous."
Shaffer's publisher, St. Martin's Press, released a second printing of the book that it said had incorporated some changes the government had sought "while redacting other text he (Shaffer) was told was classified."
From single words and names to entire paragraphs, blacked out lines appear throughout the book's 299 pages.
CNN obtained a memo from the Defense Intelligence Agency dated August 6 in which Lt. Gen. Ronald Burgess claims the DIA tried for nearly two months to get a copy of the manuscript. Burgess said the DIA's investigation "identified significant classified information, the release of which I have determined could reasonably be expected to cause serious damage to national security."
Burgess said the manuscript contained secret activities of the U.S. Special Operations Command, CIA and National Security Agency.
Shaffer's lawyer, Mark Zaid, said earlier this month that the book was reviewed by Shaffer's military superiors prior to publication.
"There was a green light from the Army Reserve Command," Zaid told CNN.
But intelligence agencies apparently raised objections when they received copies of the book.
The Pentagon contacted St. Martin's Press in early August to convey its concerns over the release of the book. According to the publisher, at that time the first printings were just about to be shipped from its warehouse. Shaffer said he and the publisher worked hard "to make sure nothing in the book would be detrimental to national security."
"When you look at what they took out (in the 2nd edition), it's lunacy," Shaffer said.
The Pentagon says Shaffer should have sought wider clearance for the memoir.