Microsoft could face further financial penalties from the European Commission - on top of a £1.3bn bill relating to a long-running competition case.
EU Competition Commissioner Joaquin Almunia issued the threat after confirming a new investigation into whether the company had met commitments it made in 2009 to give Windows operating system users a choice of web browsers other than just Microsoft's own Internet Explorer.
Soon after the announcement, in Brussels, the tech firm moved to avert a potentially costly sequel to the initial probe by admitting it had "fallen short" of its responsibility.
Its statement said: "Due to a technical error, we missed delivering the Browser Choice Screen (BCS) software to PCs that came with the service pack 1 update to Windows 7."
The company said that PCs running the original version of Windows 7, as well as Windows XP and Windows Vista, did have the screen.
"While we have taken immediate steps to remedy this problem, we deeply regret that this error occurred and we apologise for it," Microsoft said.
Microsoft had submitted a report to the Commission in December saying the browser choice screen was being provided as required.
In its statement, the company said it believed at the time that was the case but it now expected a fix to be implemented by the end of the week after discovering the error at the beginning of July.
Almunia had told reporters that if his concerns were realised, it would be the first time such a legally binding agreement with the EC had not been followed.
"Needless to say, we take compliance with our decision very seriously," he said.
"If the infringement is confirmed, there will be sanctions."