Visa charges retailers so-called multilateral interchange fees (MIFs), but the European Commission said it had sent a "supplementary statement of objections" -- opening a new chapter in a legal battle.
A statement said the Commission's "preliminary view" that these fees amount to a restriction of competition between banks and an infringement of antitrust rules prohibiting cartels.
The fees apply to all cross-border transactions in the European Union and other territories integrated into the single market, as well as domestic purchases in Belgium, Hungary, Ireland, Italy, Luxemburg, Malta, the Netherlands and Sweden.
"Visa's MIFs harm competition between acquiring banks, inflate the cost of payment card acceptance for merchants and ultimately increase consumer prices," the statement said.
In May, the EU won court backing for similar findings in a related case against MasterCard.
Visa's credit and debit cards account for some two-fifths of all payment cards issued in Europe.
The total value of spending in 2010 on cards in Europe was 1,800 billion euros, according to EU figures.
Visa Europe offered commitments to cap its debit card MIFs at 0.20 percent, which the Commission made binding in December 2010.