The European Commission is looking at whether the publishers, which include Harper Collins, Penguin and Simon & Schuster, have acted in breach of EU antitrust rules that prohibit cartels and restrictive business practices.
The EC investigation follows an inquiry earlier this year by the Office of Fair Trading (OFT).
Surprise inspections of the premises of several companies working in the e-book publishing sector were carried out by the Commission in March.
Other publishers being investigated include France’s Hachette Livre and German company Verlagsgruppe Georg von Holtzbrinck.
A statement by the EC said: "The opening of proceedings means that the Commission will treat the case as a matter of priority. It does not prejudge the outcome of the investigation.
"The Commission will in particular investigate whether these publishing groups and Apple have engaged in illegal agreements or practices that would have the object or the effect of restricting competition in the EU or in the EEA.
"The Commission is also examining the character and terms of the agency agreements entered into by the above named five publishers and retailers for the sale of e-books. The Commission has concerns, that these practices may breach EU antitrust rules that prohibit cartels and restrictive business practices."
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