Apple’s Commitment to Customer Privacy
From a press statement Apple released regarding US government requests for personal information:
conversations which take place over iMessage and FaceTime are protected by end-to-end encryption so no one but the sender and receiver can see or read them. Apple cannot decrypt that data.
So in short, Apple has reiterated (as of June 2013) that FaceTime calls and iMessages are secure and private, even from Apple. Even they cannot decrypt these communications.