In what will probably just be seen alongside this year’s string of high-visibility hacks against U.S. government targets, a top Pentagon official acknowledged Thursday that the Department of Defense has suffered one of the most damaging cyberattacks in its history.

Deputy Defense Secretary William J. Lynn III disclosed that over 24,000 files had been lost to foreign intruders in the wake of a cyberattack and security breach in March. During his speech calling for the roll out of the Pentagon’s new cyber defense strategy, Lynn mentioned that the files had been taken from a defense contractor. However, neither the disposition and identify of the attackers nor the nature of the files taken have been commented on.

The Washington Post brings us the skinny on this and other past attacks,

Lynnsaid that, over the past few years, all manner of data has been stolen, some of it mundane, some of it concerning “our most sensitive systems, including aircraft avionics, surveillance technologies, satellite communications systems, and network security protocols.”

“It is a significant concern that over the past decade, terabytes of data have been extracted by foreign intruders from corporate networks of defense companies,”Lynnsaid.

Last August, the Pentagon acknowledged for the first time that theU.S.military had suffered a major cyberattack in 2008 after malicious code was placed on a flash drive inserted into aU.S.military laptop. The code spread undetected on both classified and unclassified systems, “establishing what amounted to a digital beachhead,”Lynnwrote last year in an article for Foreign Affairs.

As we’ve seen, affiliated companies and contractors are amid the weakest links in the defense chain when it comes to cyberattacks. If we follow the recent spree of highly publicized hacks against FBI affiliates using primitive scriptkiddie antics such as AntiSec hacks of IRC Federal and Anonymous leaks from Booz Allen Hamilton, we see a grim picture painted of the security of systems external to the Department of Defense and FBI. Yet this is nothing compared to stunningly sophisticated hacking that involves breaking security and cryptographic defenses, such as when hackers used breached RSA SecurID tokens to access the networks of defense contractors such as Lockheed Martin and Northop Grumman.

“The cyber threats we face are urgent, sometimes uncertain and potentially devastating as adversaries constantly search for vulnerabilities,” Lynn said in a statement. “Our infrastructure, logistics network and business systems are heavily computerized. With 15,000 networks and more than seven million computing devices, DoD continues to be a target in cyberspace for malicious activity.”

In a bout of good timing, U.S. Senator John McCain proposed a special committee to tackle the lack of good cyber security in the wake of the hacks against IRC Federal, Booz Allen Hamilton, and others.

Where exactly is the United States Cyber Command when we need them most? Perhaps it’s about time that computer security at highly sensitive installations got treated a lot more like physical security by compartmentalizing, authenticating, and deeply encrypting everything. So that when breaches do happen (and they will anyway) at least attackers will get very few files, and those files will be buried under layers of discouraging encryption so deep they might just give up and go home.