The charge sheet was sent on June 23, it said. MasterCard will be able to respond before the Commission rules whether the company has broken EU law.
The Commission said such a ruling could end MasterCard's fees if regulators believe that any benefits of the fees are outweighed by "restrictive effects on price competition between merchant banks."
It is the second time EU regulators have accused MasterCard of breaking antitrust rules. In September 2003 they filed charges against MasterCard's cross-border interchange fees paid by merchant banks to card-issuing banks for payments made with a MasterCard or a Maestro card.
The Commission has also been pushing for a single European payment area so customers would pay the same price to make payments or transfer money to or from another country in the 12-nation euro area.
It wants to see the same fees charged for domestic and cross-border retail payments by 2010, saying this will increase trade across borders and help boost Europe's economy.
Some 45 percent of all credit or debit cards issued in the EU are MasterCard or Maestro, the AP reports.
MasterCards are accepted by some 85 percent of EU retailers who take debit card payments. In 2004 a total of 23 billion card payments were made in the EU, with an overall value of Ђ 1.35 trillion (US$1.69 trillion), the Commission said.
In a weary world of endless US military interventions, sanctions, trade tariffs and chaos, let’s pause and take stock of the shining house on the hill