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The attacks prompted senior military leaders to take the exceptional step of briefing President George W. Bush this week, according to the Los Angeles Times.
Such attacks may have originated in Russia -- an incursion that posed unusual concern among commanders and raised potential implications for national security, the paper noted.
Defense officials would not describe the extent of damage inflicted on military networks but said the attack struck hard at networks within U.S. Central Command, the headquarters that oversees U.S. involvement in Iraq and Afghanistan, and affected computers in combat zones, said the paper.
The attack also penetrated at least one highly protected classified network.
The most recent attack involved an intrusive piece of malicious software, or "malware," apparently designed specifically to target military networks, according to the paper.
"This one was significant; this one got our attention," the paper quoted an unidentified defense official as saying.
Although officials are withholding many details, the attack underscores the increasing danger and potential significance of computer warfare, which defense experts say could one day be used by combatants to undermine even a militarily superior adversary, the paper said.
Bush was briefed on the threat by Navy Adm. Michael G. Mullen, chairman of the Joint Chiefs of Staff. Mullen also briefed Defense Secretary Robert M. Gates, said the paper.
Military electronics experts have not pinpointed the source or motive of the attack and could not say whether the destructive program was created by an individual hacker or whether the Russian government may have had some involvement, the paper said.
Suspicions of Russian involvement come at an especially delicate time because of sagging relations between Washington and Moscow and growing tension over U.S. plans to develop a missile defense system in Eastern Europe, said the paper.