In a statement of objections, the EC says its preliminary view is that multilateral interchange fees set by Visa "restrict competition between banks for accepting consumer payment cards without benefiting consumers by contributing to technical and economic progress".
Last March the EC launched a probe into whether the interchange fees charged by Visa Europe "forbid restrictive business practices such as price fixing".
The investigation's launch followed the expiry of a 2002 antitrust agreement between the card company and the EU's Competition Commission when Visa agreed to reduce levels of interchange fees for processing card transactions in return for immunity from legal action.
In January Visa Europe CEO Peter Ayliffe said he expected to reach an agreement with the commission by the end of the year and the firm recently adopted a new methodology for setting cross-border fees, cutting the average from 0.7% to 0.61%.
But, although the EC says the changes are a "step in the right direction", they "do not remove its concern that Visa's MIFs restrict competition".
"Visa's MIFs harm competition between acquiring banks, inflate the cost of payment card acceptance for merchants and ultimately increase consumer prices," says the commission.
Last week the commission reached an interim agreement with MasterCard capping fees at 0.3% for credit cards and 0.2% for debit cards.