The previously classified incident, which took place in 2008 in the Middle East, was disclosed in a magazine article by Deputy Defense Secretary William J. Lynn and released by the Pentagon Wednesday.
He said a "malicious code" on the flash drive spread undetected on both classified and unclassified Pentagon systems, "establishing what amounted to a digital beachhead, from which data could be transferred to servers under foreign control."
"It was a network administrator's worst fear: a rogue program operating silently, poised to deliver operational plans into the hands of an unknown adversary," Lynn wrote in an article for Foreign Affairs. "This ... was the most significant breach of U.S. military computers ever and it served as an important wake-up call."
The Pentagon operation to counter the attack, known as Operation Buckshot Yankee, marked a turning point in U.S. cyberdefense strategy, Lynn said.
In November 2008, the Defense Department banned the use of the small high-tech storage devices that are used to move data from one computer to another. The ban was partially lifted early this year with the approval of limited use of the devices.
Lynn did not disclose what, if any, military secrets may have been stolen in the 2008 penetration of the system, what nation orchestrated the attack, nor whether there were any other repercussions.The article went on to warn that U.S. adversaries can threaten American military might without building stealth fighters, aircraft carriers or other expensive weapons systems.
"A dozen determined computer programmers can, if they find a vulnerability to exploit, threaten the United States' global logistics network, steal its operational plans, blind its intelligence capabilities, or hinder its ability to deliver weapons on target," Lynn wrote.
"Knowing this, many militaries are developing offensive capabilities in cyberspace, and more than 100 foreign intelligence organizations are trying to break into U.S. networks," he said.
Defense officials have said repeatedly that the military system of some 15,000 computer networks and seven million computers suffers millions of probes a day with threats coming from a range of attackers from routine hackers to foreign governments looking to steal sensitive information or bring down critical, life-sustaining systems.