After seemingly ending local transmissions for weeks, new infections have hit triple figures on a daily basis in the densely packed finance hub -- sparking fears the new outbreak is spreading out of control.
More than 1,000 infections have been confirmed since early July -- more than 40 percent of the total since the virus first hit the city in late January.
Some health experts have blamed an exemption from the usual 14-day quarantine which the government granted to "essential personnel", including cross-boundary truckers and air and sea crew.
Because of its extensive air links and busy port, Hong Kong is a popular transit point for ships to change crews.
The government announced a slew of measures to tighten quarantine exemptions on Sunday as the city recorded 128 new cases in the previous 24 hours, bringing the total to 2,634 with 18 deaths.
Most of the new cases were locally transmitted.
From Wednesday, only vessels with freight destined for Hong Kong will be able to change crews, but even they will not be allowed to mingle in public and must go straight to or from the airport, or stay in a designated quarantine venue.
"We believe by tightening up the relevant requirements, we can properly address the public concern on the health risk," a government spokesperson said.