The Cupertino-based firm’s mapping application arrived to a chorus of criticism when it launched last week, with users reporting missing locations, a faulty search function and blurred satellite images as their main bugbears.
Earlier this week, the company responded by releasing a public statement, claiming the app is still in its infancy and will be developed off the back of customer feedback.
In a letter posted on Apple’s website, Cook said: "At Apple, we strive to make world-class products that deliver the best experience possible to our customers. With the launch of our new Maps last week, we fell short on this commitment."
"We are extremely sorry for the frustration this has caused our customers and we are doing everything we can to make Maps better."
It’s an unprecedented move by Apple, simply because the firm rarely publicly apologises. And in another shocking twist, Cook even encouraged iPhone owners to use alternative software - including Google's Maps.
He said: "While we’re improving Maps, you can try alternatives by downloading map apps from the App Store like Bing, MapQuest and Waze, or use Google or Nokia maps by going to their websites and creating an icon on your home screen to their web app."
It comes just days after former Google chairman Eric Schmidt publicly announced that Google isn't working on its own mapping application for the iOS 6 platform, despite a series of rumours suggesting otherwise.