The warning from the Federal Office for Information Security comes after Microsoft admitted IE was the weak link in recent attacks on Google's systems.
Microsoft rejected the warning, saying that the risk to users was low and that the browsers' increased security setting would prevent any serious risk.
However, Graham Cluley of anti-virus firm Sophos, told BBC News that not only did the warning apply to 6, 7 and 8 of the browser, but the instructions on how to exploit the flaw had been posted on the internet.
