As well as the tech giant, the inquiry centres on Hachette Livre, Penguin, Harper Collins, Simon & Schuster and Verlagsgruppe Georg von Holzbrinck.
The Commission said it would focus on alleged illegal agreements restricting competition in the EU.
The UK's Office of Fair Trading has already carried out a similar inquiry.
The character and terms of agreements that the companies made with agencies are to be examined for breaches of EU rules on cartels, the Commission said.
The Office of Fair Trading has now finished its own investigation, but continues to work closely with the Commission, which is extending the scope of the inquiry across the whole of Europe.
The Commission carried out "unannounced inspections" on the companies in March 2011 as part of its investigations at premises in several European countries.
Apple's iBook store, which supplies e-books to the company's iPad tablet computer and the iPhone, is likely to come under scrutiny.
The EU announced an investigation into Google for potential anti-competitive behaviour in November.
Apple and five publishers are to be investigated over anti-competitive practice in the e-book market, says the European Union's anti-trust watchdog.