Unless Microsoft drops some features from its new Windows XP package, "a fine is a possibility", said Monti.
However, the commissioner expressed regret that a confidential document detailing the regulators' objections was leaked to the Wall Street Journal. He also played down the paper's claim for the size of the penalty.
The allegations of attempting to mislead focus on a series of letters from customers that were supplied by Microsoft to the competition commission.
Citing the document outlining its case, the newspaper claimed the Commission alleged that Microsoft had misled investigators and sought to obstruct the case. As a result, the newspaper said, the commission would impose the largest fine it could.
But speaking at a news conference, Monti dismissed the Wall Street Journal's claims that the fine could be amount to 10% of the company's annual revenue, or £1.75bn.
"To speak of fines when Microsoft has not even replied is premature. To enter this game of calculating a fine does no service to the public at large," he said.
Microsoft has been given a little extra time to make its response to the case.
In August, the EU confirmed that it had merged two antitrust investigations into Microsoft's operating systems, and that it was in the process of determining if the company had violated European antitrust rules by "using illegal practices to extend its dominant position in the market for personal computer operating systems into the market for low-end server operating systems."
The EU has charged that Microsoft has actively attempted to dominate the corporate and Internet computer software market with its Windows and Office software while also attempting to put a stranglehold on competing software for operating music and video over the Web, all in violation of European antitrust laws.
The report comes the day after the US Supreme Court rejected Microsoft's appeal to overturn a lower court's ruling that the company violated antitrust laws.