The Marine Products Association said the ban announced on Tuesday would damage a business that had already been contracting for two decades because of environmentalists' global campaigns against the harvesting of shark fins.
Chairwoman Choy Mei-kuen said the ban amounted to a "smear campaign" that would lead Hongkongers to believe the shark fin business was "worse than committing a crime like drug trafficking".
More Hongkongers would stop eating shark's fin as a result, she said.
Under Cathay's new policy, it will accept cargo orders only when merchants provide proof that their products were independently verified as sustainable shark and shark-related products. The airline expects the transition to the new policy to take about three months.
Choy said: "We are not stealing or robbing anyone to make money. The Hong Kong government has not banned the import and export of shark fin. This business is not illegal. How can Cathay Pacific decide on a ban without even consulting us?''