In 2014, the Commission ended another investigation into the company's fee structure when Visa Europe agreed to cap the transaction fees it charged.

The Commission said it was now looking at so-called inter-regional interchange fees, those charged to merchants when accepting Visa cards issued outside the European Economic Area (EEA), for example when tourists make purchases in the EU.

"Inter-regional fees represent an important part of the total fees within the Visa scheme," the Commission said.

The Commission, which has the power to fine Visa up to 10 percent of its global turnover if it is found breaching the bloc's antitrust rules, said it was waiting for the company's response before deciding on further action.

After Visa is given access to the Commission's file on the issue, it has two months to reply.

(Reporting by Robert-Jan Bartunek; Editing by Alissa de Carbonnel and Mark Potter)