"Every day, billions of dollars change hands and countless decisions are made on the basis of our likes and dislikes, our friends and families, our relationships and conversations, our wishes and fears, our hopes and dreams. These scraps of data, each one harmless enough on its own, are carefully assembled, synthesized, traded and sold," Cook said.
Zuckerberg fired back against this criticism on the earnings call.
"It's worth noting that one of the main reasons people prefer our services, especially WhatsApp, is because of its stronger record on privacy," Zuckerberg said.
"WhatsApp is completely end-to-end encrypted, does not store your messages, and doesn't store the keys to your messages in China or anywhere else. And this is important because if our systems can't see your messages, then that means that governments and bad actors won't be able to access them through us either."
On the call, Zuckerberg said the "vast majority of growth" in sharing content on its platforms are coming from its messaging services and Stories features. People send around 100 billion messages per day, and people share more photos, videos and links on WhatsApp and messenger than they do on social networks, he added.
Facebook's former head of Messenger, David Marcus, previously told CNBC Messenger wanted to be the default messaging app, replacing iMessage and Android Messages on people's phones. Marcus now heads up Facebook's blockchain initiatives.
The remarks came as Facebook discussed its third quarter earnings report on Tuesday. The company surpassed analysts' estimates on earnings per share, but fell short on revenue and active user projections. The company's shares swung wildly during its earnings call as it discussed 2019 spending projections.