He contrasted this with the stance that Apple took against the FBI last year when a court demanded that Apple provide access to data on an iPhone, which had been used by one of the terrorists involved in the San Bernardino attack in December 2015, where he claimed that the law had been on Apple's side.
In a statement issued overnight, Cook said the Chinese central government started tightening the regulations associated with VPN apps in 2015.
"We have a number of those on our store. Essentially, as a requirement for someone to operate a VPN they have to have a licence from the government there," he said.
Cook said that there were still hundreds of VPN apps in the App Store, including hundreds by developers outside China.
"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. "We strongly believe in participating in markets and bringing benefits to customers is in the best interest of the folks there and in other countries as well."
Cook claimed Apple believed in engaging with governments even when it disagreed.
"(In) this particular case, we’re hopeful that over time the restrictions we’re seeing are loosened, because innovation really requires freedom to collaborate and communicate," he said.
"I know that is a major focus there. That’s sort of what we’re seeing from that point of view. Some folks have tried to link it to the US situation last year. They’re very different.
"In the case of the US, the law in the US supported us. It was very clear. In the case of China, the law is very clear there. Like we would if the US changed the law here, we have to abide by them in both cases. That doesn’t mean that we don’t state our point of view in the appropriate way, we always do that."