A crackdown on moorings means hundreds of boat owners could see their vessels left at the mercy of the typhoon season.
The Marine Department has stepped up enforcement of rules regarding boat length and ownership of moorings.
Where owners are found in breach of the regulations, they are being given just two weeks' notice to move their boats.
And with a chronic shortage of sheltered moorings, it means many vessels could be left without a safe haven.
The action comes at a time when boat owners fear rents at some privately held moorings could soon more than double.
Paul Zimmerman, a Southern district councillor and chief executive of Designing Hong Kong, urged the government to create public marine centres.
"We need to address the shortfall of safe moorings for the increasing number of boats used for tourism, pleasure, recreation and sports," he said. "This shortfall of moorings makes it impossible for people - except for the super-rich - to enjoy Hong Kong's magnificent shorelines and beautiful waters."
The department has issued warning letters to hundreds of boats in Aberdeen Harbour for exceeding the lengths designated for their moorings. Many moorings are for vessels up to 19 feet, but a lot of the boats exceed this.
Owners of the moorings were also reminded they must be the owners of the boats using those moorings, to prevent problems created by rampant sub-letting.
Owners in breach of the rules are being given two weeks to vacate their moorings. The department refused to extend the notice period until the end of the typhoon season in November.
The marine authorities said they were only enforcing the law. Every private mooring should be used only by the designated vessel, they confirmed.
"Moreover, any oversized vessel may also cause obstruction to other vessels," a department spokesman said. "Owners will be required to remove any oversized vessel from the private mooring within 14 days."
Failing this, the department had the power to remove the vessel itself and re-allocate the berth.
Kandy Chan, manager of the Sun Hing Shipyard at Po Chong Wan Road, Aberdeen, agreed the government had to act fast to avert further problems. "Along the coastline between Kwun Tong and where the old Kai Tak airport used to be is a perfect area to erect temporary and permanent moorings for pleasure boats," she said.
"In the long term, expanding the Aberdeen Typhoon Shelter would also create new moorings."