Apple has been in a legal battle with the FBI, which is trying to extract information from the iPhone of one of the accused shooters of last year's San Bernardino attack.
Cook said on stage today that he wished to address a subject in "everyone's" mind.
"We need to decide as a nation how much power the government should have over our data and over our privacy," Cook said. "I have been humbled and deeply grateful for the outpouring of support we have received from Americans across the country from all walks of life," he said, adding the company never expected to be "at odds with our own government."
“We did not expect to be in this position, at odds with our own government. But we believe strongly that we have a responsibility to help you protect your data and protect your privacy. We owe it to our customers and we owe it to our country,” Cook said.
“This is an issue that impacts all of us and we will not shrink from this responsibility," Cook said.