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"Nintendo, together with seven of its main European distributors, colluded to prevent imports of the games from one European market to another," commission spokeswoman Amelia Torres said.
Torres added that the illegal practices occurred between 1991 and 1998.
The price of Nintendo's games varied widely between the 15 European Union member states. For example, in 1996, prices in the UK were 65% cheaper than the prices charged for the same products in Germany and the Netherlands.
Torres said the cartel "prevented millions of European citizens from being able to buy Nintendo games at the cheapest prices".
Nintendo said it would appeal against the commission decision. While it has accepted that its distribution practices did not comply with EU competition rules and had accounted for the decision in its financial planning, it has found the size of the fine "surprising".
The appeal comes a week after the commission lost two appeals of its competition rulings in the Court of First Instance in Luxembourg, Europe's second-highest court.
Nintendo for its financial year to March 2002 reported ¥116.16bn (£562m) in sales to European customers, 20.9% of its total sales to customers outside Japan.
The seven Nintendo distributors also fined by the commission are John Menzies in the UK, Concentra - Produtos para crianças (Portugal); Linea (Italy); Bergsala (Sweden); the Greek unit of Japan's Itochu; Nortec (Greece); and the Belgian unit of Germany's CD-Contact Data.
The distributors were together fined €18.8m (£12m) for their role in the cartel.