The tech giant is pushing ahead with its legal action against Corellium - which virtualizes iOS software and claims it helps security researchers find bugs in the platform - and has amended the lawsuit, alleging copyright infringement.
The process of jailbreaking lets users modify Apple's operating systems to remove restrictions and give more options to customize the interface.
In a statement, Apple said: "Corellium's conduct plainly infringes Apple's copyrights.
"It simply copies everything: the code, the graphical user interface, the icons - all of it, in exacting detail.
"This is not a case in which it is questionable or unclear whether the defendant reproduced the rights-owner's works, or more subtly, whether particular portions of the works that the defendant took are ultimately protected by federal copyright law."
However, Corellium chief executive Amanda Gorton has responded in an open letter and criticized the company's response.
She argued: "Apple is asserting that anyone who provides a tool that allows other people to jailbreak, and anyone who assists in creating such a tool, is violating the DMCA (Digital Millennium Copyright Act).
"They have directly benefited from the jailbreak community in a number of ways. Many of the features of iOS originally appeared as jailbreak tweaks and were copied by Apple."