"While we have taken immediate steps to remedy this problem, we deeply regret that this error occurred and we apologise for it," the US company said in a statement.
In order to ease EU competition concerns in 2009, the US software giant committed to provide Windows users in Europe a "choice screen" enabling them to choose a web browser instead of Microsoft's default Internet Explorer.
"We have fallen short in our responsibility to do this," Microsoft said.
The European Commission warned that Microsoft could face a fine if an infringement were discovered.
Microsoft said that due to a "technical error," it failed to deliver the "browser screen choice" (BCS) software to PCs that came with a service pack 1 update to the Windows 7 operating system.
This mistake left 28 million PC owners without the choice to choose an alternative to the default Internet Explorer browser, Microsoft said.
The company said it developed software to fix the problem on July 2, one business day after it discovered the problem.
"We expect to substantially complete distribution of the BCS software to the PCs we initially missed by the end of the week," the statement said.
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