On Friday night, the Civil Aviation Administration of China said that Cathay crew who have engaged in the protests pose a threat to aviation safety in mainland China, according to a statement on its website.
The aviation authority ordered Cathay to provide identification information for its crew on mainland-bound flights.
Crew members that have not gained the authority's approval will not be allowed into its airspace, including on flights bound for other destinations.
The airline has also been ordered to draw up proposals to strengthen safety and security, said the statement.
In response, a Cathay Pacific spokesperson said: "We have received the directive and are studying it very carefully. We are treating it seriously and are following up accordingly."
"The safety of our passengers is always the top priority of Cathay Pacific. There is zero tolerance for any inappropriate and unprofessional behaviour that may affect aviation safety. We deal with these incidents very seriously."
Cathay said on Thursday it respects "everyone's right to express themselves in a peaceful and respectful manner," while insisting it "recognises that Hong Kong SAR is a part of China".
"We do not condone any activities that jeopardise the stability of Hong Kong," it said.
On Monday aviation workers joined a strike that gridlocked Hong Kong, forcing airlines, including Cathay, to cancel hundreds of flights.
Responding to a question on the protests at a press conference earlier this week, Cathay chairman John Slosar said the company respects its staff's opinions.
"We certainly wouldn't dream of telling them what they have to think about something. They're all adults, they're all service professionals. We respect them greatly," he said.
Global Times, published by the Communist Party's official People's Daily, ran news stories this week highlighting Cathay employees' participation in the ongoing protests.
Embattled Hong Kong chief executive Carrie Lam on Friday urged an end to the violence, claiming that the protests are dragging on the city's economy.
Hong Kong-listed Cathay is 45% owned by Swire Pacific and 22.7% held by Air China, according to Refinitiv Eikon.
The airline has been Hong Kong's flag carrier since the colonial era. Swire Pacific's parent, John Swire & Sons Ltd, is a UK-based conglomerate with businesses ranging from property to transportation.
(Additional reporting by Donny Kwok, Twinnie Siu, Tom Westbrook, Lina Juarawee in HONG KONG, Brenda Goh in SHANGHAI and Beijing Monitoring Desk; Writing by Noah Sin; editing by Jan Harvey and Jason Neely) ((Noah.Sin@thomsonreuters.com; +852 2841 5782; Reuters Messaging: email@example.com; Twitter: https://twitter.com/noah_sin))