The Federal Office for Information Security, or BSI, issued the warning to Germans after the security hole led to hacks against Google and others.
"The attacks on Google were by highly motivated people with a very specific agenda," Thomas Baumgaertner, a spokesman for Microsoft in Germany was quoted by BBC News as saying.
He said, "These were not attacks against general users or consumers. There is no threat to the general user, consequently we do not support this warning."
Microsoft said that the hole could be closed by setting the browser's Internet security zone to "high."
However, German authorities say that even with this modification, IE would not be fully safe.