The positive test result triggered a lockdown at Towers 1, 2 and 3 of Hampton Place in Tai Kok Tsui, where the man lives.
Cathay also said it had arranged another Frankfurt hotel for air crew.
Health officials said the aircrew member was carrying the L452R mutant strain linked to the more infectious Delta variant after returning to Hong Kong on November 7.
Cathay said it was conducting a thorough internal investigation “to ensure we continue to operate with the highest degree of safety and compliance”.
The airline said it would also step up compliance checks at overseas stations to ensure its health and safety protocols were being strictly followed by aircrew during their layovers.
Cargo pilots are exempt from hotel quarantine, but after two other Cathay ones tested positive with the Delta variant earlier this week, fears are growing that the exemption could spark new community cases and derail efforts to match the mainland’s zero-Covid approach and fully reopen the border.
The government said on Friday that it would tighten infection-control measures for flight crew members, after two of them were among the city’s recent imported Covid-19 patients.
All local air crew staff are required to get the third dose of vaccine.
Cargo crew members will be subject to daily testing upon their return to Hong Kong and stricter restrictions will be imposed during their medical surveillance period. Airlines have also been asked to assign monitoring staff to ensure crew members comply with a closed-loop system when they work overseas.
On Wednesday, health officials said that two other Cathay cargo pilots had tested positive for Covid-19 upon their return from Frankfurt last Saturday and were staying at home in Tsim Sha Tsui and Discovery Bay.
Their household members and close contacts were quarantined, including 120 students at Discovery Bay International School, where the wife of one of the pilots teaches and their two sons attend, and 13 other close contacts of the Cathay worker. Sixty friends and colleagues of the other pilot were also quarantined.