Kroes was unhappy that Microsoft has accused the European Commission of colluding with its rivals, during the on-running antitrust trial.
"If we pursue the line we are following now, there will be fines and they won't be small fines," said Kroes on Thursday, according to the Financial Times.
On Thursday, Microsoft said the EC had held back documents that the software giant needs in order to defend itself against a possible antitrust fine of up to 2 million euros a day.
Microsoft also said that the EC had encouraged other companies to have "extensive, unsupervised and undocumented contact" with the Dr Neil Barratt. Barratt is a UK computer expert who was appointed as a trustee to monitor Microsoft's compliance with the EC antitrust ruling of 2004.
"The Commission also took it upon itself to facilitate secret meetings between the Trustee and another of Microsoft's adversaries... The purpose of the meetings was to allow [the adversary's] engineers to work together with the Trustee on identifying "any continuing gaps, which would allow the Trustee to demand supplementary information from Microsoft," claimed Microsoft.
Microsoft published its latest claims on its Web site.
ZDNet UK's Graeme Wearden reported from London. For more coverage from ZDNet UK, click here.
