Officers believe the vessels and the engines are worth more than HK$25 million in total.
At a press briefing on Sunday, assistant district commander Chong Shing-yat said the biggest vessel was 15 metres long and had six outboard motors fitted, which allowed it to travel at up to 60 knots, or 110 kilometres, per hour.
He said the operation was conducted on Thursday, and it was the first time officers had seized so many outboard engines in a single operation.
Chong added the vessels are probably planned for smuggling goods or people.
The warehouse on Lung Ku Tan Road in which the vessels were found was located at a remote location, and was hidden behind containers, making it more difficult for officers to find them, Chong said.