The unclassified email network used by General Martin Dempsey, chairman of the Joint Chiefs of Staff, and hundreds of military and civilian personnel was taken offline over the weekend, the Pentagon told CNN.
Officials will not say exactly what happened, but the US military's Cyber Command is now investigating the matter according to Lieutenant Colonel Valerie Henderson, a Pentagon spokesman.
So far, there is no indication any classified systems were impacted, officials said.
Right now the focus is on "mitigating the cyber security risks we see across our impacted network," the official said.
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The report comes days after the FBI said the US has witnessed a 53 per cent spike in economic espionage cases aimed at American firms, with a vast majority of the perpetrators originating from China with ties to the government.
The head of the Federal Bureau of Investigation's counterintelligence division, Randall Coleman, said there has been a 53 per cent increase in economic espionage cases, or the theft of trade secrets leading to the loss of hundreds of billions of dollars, over the past year.
He cited examples of large corporations successfully targeted in the past such as DuPont, Lockheed Martin and Valspar, who have since worked with the FBI to further safeguard their intellectual property.