In a supplementary statement, the Commission says that its preliminary view is that the Visa multilateral interchange fees (MIFs) for consumer credit cards violate its rules designed to stop cartels and restrictive business practices.
The EC says it thinks that MIFs "harm competition between acquiring banks, inflate the cost of payment card acceptance for merchants and ultimately increase consumer prices".
It also "doubts" that Visa's MIFs are "necessary to create efficiencies that benefit merchants and consumers" and could therefore be entitled to an exception from the rules.
The supplementary statement is the latest stage in a lengthy battle that saw Visa slash its multilateral interchange fees for debit cards in late 2010 but refuse to back down credit cards.
Visa can now make a written reply or ask for a hearing on the issue which could see fines imposed of up to 10% of turnover imposed for antitrust breaches,
Responding to the new development, Peter Ayliffe, CEO, Visa Europe, says: "We are very disappointed that the Commission has taken such a confrontational approach and was not willing to find a solution to support investment and innovation in European payments for the benefit of European consumers and to allow European payments to compete globally."
In May an EU court dismissed Visa rival MasterCard's challenge against an EC ruling that the firm's cross-border interchange fees for both credit and debit cards violated competition law.
Meanwhile, both card giants are facing interchange problems in the US: having agreed a $7.25 billion class action settlement with retailers earlier this month, several major merchants, including Walmart, have now come out against the plan.