The southern Chinese city is one of the world's biggest markets for shark fins, which are used to make soup that is an expensive staple at Chinese banquets and viewed by many Asians as a rare delicacy.
Activist Gary Stokes who has visited the site estimated there are 15,000 to 20,000 fins being laid to dry on the rooftop on Hong Kong island ahead of an anticipated surge in demand over Lunar New Year in February this year.
"This is shocking," the Hong Kong coordinator for conservation group Sea Shepherd told AFP.
He said it was the first time he had spotted such a massive hoarding of shark fins in one place in the Asian financial hub.
"This is the most graphic, brutal and barbaric part of the industry - the element of chopping a shark's fin off and throw it back into the water is horrific and inhumane."
Mr Stokes believed the large amount of shark fins were destined for China, and that traders moved to dry the shark fins on secluded rooftops instead of sidewalks - as they have done in the past - to avoid public anger.
Campaigns against consuming shark fins have gained ground in Hong Kong in recent years, after major hotel chains decided to drop the soup from the menus, and home carrier Cathay Pacific said in September it would stop carrying unsustainable sourced shark products on its cargo flights.
"The demand in Hong Kong is definitely decreasing but unfortunately, the demand in China is growing," Mr Stokes said.
"As long as there is no protection for the sharks, the (demand) will just keep going on and on," he added.
Environmentalists say the sustainable shark fin industry is tiny and most of the products are harvested in a way that threatens scores of shark species deemed vital for healthy oceans.
About 73 million sharks are killed every year, with Hong Kong importing about 10,000 tonnes annually for the past decade, according to environmental group WWF. Most of those fins are then exported to mainland China.
The number of threatened shark species has soared from 15 in 1996 to more than 180 in 2010, mainly due to the growing Chinese demand for fins.