The airline said Saturday that employees who "support or take part in illegal protests, violent actions, or overly radical behaviour" would be barred from crewing flights to mainland China. It also confirmed that one of its pilots was removed from his duties since July 30.
The pilot was reportedly among over 40 people charged with rioting, during clashes with police near Beijing's main representative office in the city.
Hong Kong — a former British colony that was returned to Chinese rule in 1997 — has been struggling to end weeks of protests that have in recent weeks turned increasingly violent and disruptive.
The rallies, which were started to protest a bill that would have allowed people to be extradited to mainland China, have snowballed into a democracy movement, with some even demanding full autonomy from Beijing.
The unrest has frequently crippled the Asian financial hub's transportation system and last Monday, Cathay cancelled hundreds of flights during a general strike.
Cathay's decision came a day after China's aviation authority issued a "major aviation safety risk warning" to the airline.
The Civil Aviation Authority said that "on multiple occasions," Cathay's flight personnel have participated in "violent assault," according to CNBC's translation.
"The incidents pose a serious threat to aviation safety, causing adverse social impact and as a result is increasing inbound aviation safety threats from Hong Kong to the mainland," it said.
It also ordered the carrier to provide identification information for its crew on mainland-bound flights, and said that crew members that do not receive the authority's approval will not be allowed into its airspace, including on flights bound for other destinations.
As the protests continue, many businesses have voiced their concerns about losing access to the world's second largest economy. Involvement by the aviation authority in China could raise more questions about whether businesses will have to take sides.
"Though people may share different views, it is essential that we all respect each other, our customers and members of the public. We have zero tolerance for inappropriate behaviour that affects the safe operation of our flights and the service experience we provide to our customers," Cathay CEO Rupert Hogg said in a statement to the staff on Saturday.
He said operations in mainland China were key to the company's businesses, and that it must comply with the China's Civil Aviation Administration requests and regulations.
Cathay owns more than 18% of China's flag carrier, Air China, which in turn holds a stake of a little under 30% of the Hong Kong carrier, according to Reuters.
The company told CNBC in an email: "We express no view whatsoever on the subject matter of any proceedings to which he (the pilot) may be subject. As always our actions and responsibilities are focused on the safety and security of our operations."
Just days before the announcement of the pilot's suspension, Cathay Chairman John Slosar said his company — which employs 27,000 staff in Hong Kong — respects different thoughts and believe that staff have the right to hold any political view as they are "all adults" and "service professionals."
"You would easily imagine that within that 27,000 we have virtually every opinion on every issue ... we certainly wouldn't dream of telling them what they have to think about something," he said at that time.
— Reuters contributed to this report.