"From February 2011 until July 2012, millions of Windows users in the EU may not have seen the choice screen," the commission said.
Microsoft blamed the failure to display the screen on a technical glitch.
"We take this matter very seriously and moved quickly to address this problem as soon as we became aware of it," the company said in a statement. "Although this was the result of a technical error, we take responsibility for what happened, and we have taken steps to strengthen our internal procedures to help ensure something like this cannot happen again. We sincerely apologize for this mistake and will continue to cooperate fully with the Commission."
Windows plans to release the next generation of its operating system, Windows 8, later this week.
The European Commission's action comes as the agency is negotiating with Google over antitrust allegations. Regulators are concerned that Google may be manipulating its search results to ensure that its own services appear above its rivals.
The Federal Trade Commission is conducting its own parallel investigation into Google in the United States.