The program has to remain secret or it would "get people killed," Woodward said on CNN's "Larry King Live."
"It is a wonderful example of American ingenuity solving a problem in war, as we often have," Woodward said Monday.
In "The War Within: Secret White House History 2006-2008," Woodward revealed the military-developed capabilities to locate, target and kill leaders of al-Qaida in Iraq and other insurgents, CNN said.
National security adviser Stephen Hadley, in a written statement on Woodward's book, acknowledged the strategy but disputed Woodward's conclusion that the surge of 30,000 U.S. troops into Iraq wasn't the primary reason for the decline in violence.
"It was the surge that provided more resources and a security context to support newly developed techniques and operations," Hadley said via e-mail.
While the effectiveness of the secret operations on reducing the violence is up for debate, Woodward told King he concluded it "accounts for a good portion."