In an earnings call for Apple's quarterly financial report, Cook said China tightened its rules on virtual private networks, or VPNs, in 2015 and was making a renewed push to enforce them.
"We would obviously rather not remove the apps, but like we do in other countries, we follow the law wherever we do business," he said Tuesday.
By helping Chinese authorities curb the use of many popular VPNs, U.S. tech companies are seen as helping the Communist Party bolster what is already the world's most elaborate and sophisticated censorship regime, often called the "Great Firewall."
In addition to blocking the likes of Google and Facebook, China's censors shape what is published online, pull content deemed politically sensitive and, according to a recent study, intercept images sent via chat apps.
Cook said pulling some apps beats pulling out of the market.
"We strongly believe that participating in markets and bringing benefits to customers is in the best interest of the folks there and in other countries, as well," he said. "And so we believe in engaging with governments even when we disagree."
Amazon.com also was in the spotlight Wednesday after disclosures that the company's Chinese partner, Beijing Sinnet Technology, sent emails to clients advising them to delete tools used to circumvent censorship. The news was first reported by the New York Times.
An employee told The Washington Post that Sinnet sent clients emails Friday and again on Monday warning them to eliminate content that violates Chinese telecom laws. The instructions came from China's Ministry of Industry and Information Technology, the employee said.
On Wednesday, calls to Amazon Web Services' China office went unanswered. (Amazon founder and chief executive Jeffrey P. Bezos owns The Post.)
When China's only winner of the Nobel Peace Prize, Liu Xiaobo, died in state custody last month, news of his death was all but scrubbed from the Web here. On some platforms, the candle emoji was blocked.
To get around these restrictions, millions of Chinese individuals and businesses use VPNs. Beijing knows this but so far has let the practice continue, in part because it is good for business and aids academic research.
It is not yet clear how the latest drive to regulate VPNs will play out. In the earnings call, Cook stressed that the company had removed some, but not all, apps. The fact that many VPNs remain could mean the government is focused on regulating the VPN industry, not eliminating it, leaving room for some use.
For a sector focused on privacy, that is still bad news.
"Apple claims to just follow the law, but it's just a convenient excuse," said Martin Johnson, the pseudonymous co-founder of GreatFire.org, a website that monitors China's Internet filtering and maintains an app to help Internet users get past the restrictions. "In fact, they are actively helping the Chinese government expand its control globally."
"When Apple removes an app from the App Store of a given country, it affects all users who have registered with an address in that country, regardless of their physical location," he added.
"This means that, thanks to Apple, Beijing gets a degree of control of Chinese citizens anywhere in the world."
Yang Liu and Shirley Feng contributed to this report.