Zuckerberg maintained that one of Facebook's problems was that it was "idealistic," focusing on the positive aspects of connecting people and that "we didn't spend enough time investing in, or thinking through, some of the downside uses of the tools."
"I think now people are appropriately focused on some of the risks and downsides as well," he said.
"I think we will dig through this hole, but it will take a few years. I wish I could solve all these issues in three months or six months, but I just think the reality is that solving some of these questions is just going to take a longer period of time."
Zuckerberg also fired back at comments last week from Cook, who argued that Facebook got into trouble because of a business model focused on monetising people's data.
"I find that argument - that if you're not paying that somehow we can't care about you, to be extremely glib. And not at all aligned with the truth," he said.
"The reality here is that if you want to build a service that helps connect everyone in the world, then there are a lot of people who can't afford to pay. And therefore, as with a lot of media, having an advertising-supported model is the only rational model."
The interview was the latest by the Facebook chief aimed at blunting the impact of a scandal over the harvesting of personal data on 50 million users by a political firm linked to Donald Trump's 2016 campaign.
Authorities on both sides of the Atlantic have launched investigations into the mishandling of user data and have been seeking Zuckerberg's testimony.