According to a questionnaire sent last week to several European mobile network operators, the Commission is focusing on distribution terms that might favour Apple by ensuring no rival can secure a better sales deal, said the newspaper.
Apple said its contracts comply with EU laws, said the FT.
The inquiry is the result of private complaints from mobile operators and is at a preliminary stage.
Before a formal probe can be launched, the Commission would need to be confident that Apple was dominant in the EU smartphone market, which may be hard to show given the popularity of Samsung Electronic's Galaxy handsets.
© Thomson Reuters 2013