Speaking at the D11 conference, Cook said the company had never considered signing the court settlement offered by the Department of Justice as all five of the accused publishers now have.
Instead, Apple will fight the allegations alone during the trial, which kicks off next month, with Cook insisting that the company did nothing wrong.
He said in the interview: "We're not going to sign something that says we did something that we didn't do, so we're going to fight."
Apple has had to watch as each of the publishers, Hachette Book Group, HarperCollins Publishers, Simon & Schuster (owned by CBS, which publishes CNET), Macmillan Publishers, and Penguin Group, chose to pay hefty settlements, rather than risk a stronger penalty in court.
Apple has always insisted there was no collusion with the publishers and Apple's iBook Store, dating back to Steve Jobs' time in charge of the company.
The settlements from the publishers now allow retailers to reduce prices, which should lead to better deals for consumers.
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A technology journalist, writer and videographer of many magazines and websites including T3, Gadget Magazine and TechRadar.com. He specializes in applications for smartphones, tablets and handheld devices, with bylines also at The Guardian, WIRED, Trusted Reviews and Wareable. Chris is also the podcast host for The Liverpool Way. As well as tech and football, Chris is a pop-punk fan and enjoys the art of wrasslin'.