The shipping trade on Tuesday complained about the ban on vessels coming to Hong Kong, except those bringing in daily goods.
Quarantine rules have also been tightened on air and sea crew who were previously exempt.
Sunny Ho, chairman of the Hong Kong Logistics Management Staff Association, said the new rules will prevent activities such as the buying and selling of boats via Hong Kong, as well as deny entry to ships which regularly stop here for fuel and water.
From Wednesday, sailors will only be allowed to travel directly between their boats and the airport or vice-versa, on transport arranged by their employers.
Crew rotation via Hong Kong will only be allowed for vessels bringing daily goods into the city.
Meanwhile, flight crews coming to Hong Kong will have to obtain proof that they had tested negative for the virus in the 48 hours before their flight to the city, or they will need to get tested at AsiaWorld-Expo upon arrival.
They will have to wait for the results at the testing centre or self-isolate at other “designated places”.
Airlines are also required to arrange transport for their staff to head home or to their hotel.
A government statement said similar rules were being brought in for anyone else exempted from quarantine.