It issued the warning as a researcher said he found evidence that suggests the hackers who exploited the flaw were seeking to attack defense contractors.
Microsoft said on Monday that attackers can exploit the bug in its Internet Explorer, used on hundreds of millions of computers, to infect the PC of somebody who visits a malicious website and then take control of the victim's computer.
The German government's Federal Office for Information Security, or BSI, said it was aware of targeted attacks and that all that was needed was to lure Web surfers to a website where hackers had planted malicious software that exploited the bug.
"A fast spreading of the code has to be feared," the German government said in its statement.
BSI advised all users of Internet Explorer to use an alternative browser until the manufacturer has released a security update.
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