Kroes said the U.S. Embassy in Brussels, Belgium, had asked her to be "nicer" to Microsoft ahead of her decision to fine($357 million) in July.
The commissioner criticized the approach. "This is of course an intervention which is not possible," Kroes told Dutch newspaper Financieele Dagblad this week.
When asked if she was annoyed by the embassy's approach, she said: "In my work, I cannot have a preference. I have, however, a personal opinion, but that is for Saturday night."
Kroes' representative added in an e-mail to CNET News.com's sister site ZDNet UK on Tuesday: "We can confirm that she was lobbied and that she did not appreciate it."
Microsoft declined to comment on Kroes' claims, but an insider insisted thatbetween the U.S. government and the EC.
The U.S. Embassy had not responded to requests for comment at the time of writing.
Microsoft was hit with the fine for failing to comply with the Commission's landmark antitrust ruling of 2004.
The Commission hadto help rivals develop server software that is fully compatible with Windows.
Microsoft has previously denied failing to comply with the terms of the antitrust ruling. Two months ago, it submitted a lengthy document which it said proved it had opened up its server interoperability protocols, as demanded by the EC.
Richard Thurston of ZDNet UK reported from London.