The commission's concerns stem from certain clauses in these contracts, which it says "seem to shield Amazon from competition." These clauses include "the right [for Amazon] to be informed of more favourable or alternative terms offered to its competitors," and "the right to terms and conditions at least as good as those offered to its competitors." Given the public declaration, it's clear the commission knows these stipulations exist, it's now just a matter of determining whether they fall under the umbrella of good business practice or anti-competitive behavior.
Today's announcement marks the second occasion the EU has waded into the e-book arena. The commission already probed Apple and a number of major publishers including HarperCollins, Hachette and Penguin Random House for colluding. All five publishers eventually agreed with its conclusions and settled.
Update: Amazon has now issued a response to today's news, saying:
"Amazon is confident that our agreements with publishers are legal and in the best interests of readers. We look forward to demonstrating this to the Commission as we cooperate fully during this process."