In an earnings call after posting robust Q3 results, Zuckerberg said late on Monday that the company did experience revenue headwinds this quarter.
"Apple's changes are not only negatively affecting our business, but millions of small businesses, and what is already a difficult time for them and the economy," he told the analysts.
Facebook has been fiercely critical of the iOS 14 changes since these were introduced some months ago.
Sheryl Sandberg, Facebook's Chief Operating Officer, said that the biggest impact to them has come from iOS 14 changes which advantaged Apple's own advertising business.
"We started to see that impact in Q2, but adoption on the consumer side ramped up by late June, so it hit critical mass in Q3. As a result, we've encountered 2 challenges," she said.
"One is that the accuracy of our ads targeting decreased, which increased the cost of driving outcomes for our advertisers. And the other is that measuring those outcomes became more difficult," Sandberg told the analysts, adding that on targeting, "we focused on improving campaign performance even with the increased limitations facing our industry".
The company said that to counter Apple, it is building commerce tools to help businesses reach more new customers, and get more incremental sales.
"Over the longer term, we're developing privacy enhancing technologies in collaboration with others across the industry to help minimise the amount of personal information we process, while still allowing us to show relevant ads," said Sandberg.