Digital civil liberties organization the Electronic Frontier Foundation is reporting that Apple is arguing that “jailbreaking an iPhone constitutes copyright infringement and a DMCA [digital millenium copyright act] violation.” These comments from Apple were filed with the U.S. Copyright Office in conjunction with the 2009 DMCA review, which happens every three years.

EFF says that this the first formal public statement by Apple about its legal stance on iPhone jailbreaking. For the uninitiated, jailbreaking is a practice in which iPhone owners break out of the built-in restrictions of the popular mobile phone in order to use applications from sources other than Apple’s own iPhone App Store.

The number of iPhone owners who have jailbroken their phones is estimated in the hundreds of thousands.

EFF has asked the Copyright Office, as part of its 2009 DMCA rulemaking, to recognize an exemption to the DMCA to permit jailbreaking in order to allow iPhone owners to use their phones with applications that are not available from Apple’s store.

Apple, for its part, argues that its copyright is infringed, in that jailbroken iPhones depend on modified versions of Apple’s bootloader and operating system software. Opening the jailbroken iPhone to applications not approved for distribution via the Apple iPhone App Store, they say, will compromise the safety and security of the iPhone, and, in EFF’s paraphrase of the argument, “swing the doors wide for those who want to run pirated software.”

EFF rebuts Apple’s argument, saying that “the courts have long recognized that copying software while reverse engineering is a fair use when done for purposes of fostering interoperability with independently created software, a body of law that Apple conveniently fails to mention.”

We’ll keep you posted on the story as it develops.