The move is in line with recent directives from Beijing's Ministry of Industry and Information Technology (MIIT), which issued orders at the beginning of the year requiring VPNs to seek licenses from the government before operating.
"We would obviously rather not remove the apps, but like we do in other countries, we follow the law wherever we do business", said Cook.
The company has been heavily criticised for removing several VPN apps, and was accused of "aiding Chinese censorship efforts". It was very clear.
"We believe in engaging with governments even when we disagree", he said. China's government made a decision to tighten the Internet restrictions in the country and ban VPNs, which also led to the removal of some VPN mobile apps of major developers, in order to meet the new regulations.
The move by Apple is another setback for internet users in China who are rapidly finding that their options for bypassing China's Great Firewall are diminishing.
Chinese authorities have clamped down on everything from internet browsing to live-streaming websites and social media in the run-up to an important Communist Party conclave in the fall, at which most of the country's top leaders are set to be replaced. But he said other options remain available for the time being.
Amazon did not respond to Reuters' requests for comment outside of USA business hours, but the firm told the Wall Street Journal that Sinnet was "responsible for ensuring that its customers in China comply with local laws". The People's Republic of China has issued a blanket ban of common websites like Facebook, Google, and many western media outlets, all of which are accessible within Russian Federation.
Mr Cook said comparisons to a legal battle in the United States previous year - in which the firm refused to help the Federal Bureau of Investigation unlock a dead terrorist's iPhone - were unfair.
The government has been intent on tightening controls domestically as well.
China said in January it would begin to restrict VPNs, and this month reportedly told the country's three big telecom companies to block individuals' access to them by early next year. Furthermore, the law will require search engines to remove references to blocked websites so citizens don't know what it is they are not allowed to see. The state doesn't really respect the idea of freedom on the internet, according to Freedom House, a nonprofit that researches human rights and ranks countries based on their appreciation of liberty. The company removed multiple apps belonging to the New York Times from the App Store in China in December.