Hong Kong chief executive Carrie Lam last week singled out the airline and ordered probes into allegations that its aircrew broke pandemic regulations.
In response, Cathay’s chairman Patrick Healy reportedly told staff that non-compliance of a “tiny minority” must not “overshadow the remarkable discipline and professionalism” of the majority of its aircrew.
Hong Kong has continually adjusted its quarantine rules for air crew as it pursues mainland China’s zero Covid policy.
The city dramatically tightened its regulations after the emergence of Omicron last year, leading to Cathay cancelling most of its planned passenger and cargo flights in January.
Even before the tougher rules were imposed the airline had been struggling to staff many of its flights, as some routes relied on pilots volunteering to fly rosters that involved being confined to hotel rooms for five weeks at a time.
Cathay pilots have previously told the BBC how the rules have affected their mental health and put a strain on their personal lives, with one saying that he was “in a perpetual state of quarantine.”