Cook's speech at a data privacy conference in Brussels did not mention Facebook by name, but the social media company was clearly a target of the Apple CEO's warning.
"If a business is built on misleading users, on data exploitation, on choices that are no choices at all, it does not deserve our praise. It deserves reform," Cook said.
Cook also criticized recommendation algorithms that suggest extremist groups to users, as Facebook has been under fire for doing. On Wednesday, Facebook said it will no longer automatically recommend political groups.
Cook also said he believes that some companies reward content that could undermine public trust in vaccinations to boost engagement.
"At a moment of rampant disinformation and conspiracy theories juiced by algorithms, we can no longer turn a blind eye to a theory of technology that says all engagement is good and the longer the better," Cook said.
The speech comes as the battle between the Silicon Valley rivals heats up, particularly about a new iPhone feature called App Tracking Transparency, which will force apps to ask for user permission to access an important device identifier that's used by companies like Facebook and Google to serve and measure mobile ads.
Cook's comments also come amid questions about whether Facebook's algorithms and tools were used to supercharge the pro-Trump riot on Capitol Hill on Jan. 6. Facebook COO Sheryl Sandberg was already forced to defend the company, saying that rioters who were planning violence were "largely" not organized on Facebook.
"It is long past time to stop pretending that this approach doesn't cover the costs of polarization, of lost trust, of violence," Cook said. "A social dilemma cannot be allowed to cause a social catastrophe."
On Wednesday, Facebook CEO Mark Zuckerberg slammed the App Tracking Transparency change, and said that Apple was its biggest competitor. He also implied that Apple is using privacy as a justification to disadvantage Facebook.
"Apple has every incentive to use their dominant platform position to interfere with how our apps and other apps work, which they regularly do to preference their own," Zuckerberg said.
Apple told CNBC on Wednesday that the next beta version of its iPhone operating system will start to enforce app tracking, which means the change will go into effect for everyone soon — Apple says it will happen in "early spring."
Correction: An earlier version of this story misquoted a sentence of Tim Cook's speech. The correct quote is: "It deserves reform."