The haul -- which included more than 1,000 elephant tusks -- was the second seizure of endangered species parts in a month in the Asian financial hub, home to one of the busiest ports in the world.
Acting on a tip off from mainland authorities on Tuesday, customs officials discovered the illicit goods hidden in a cargo container at the city's Kwai Chung terminal port.
The container was officially declared to contain "red cam process wood" exported from Nigeria.
"Among the wooden blocks, we found 21 wooden crates and inside these crates, we found 1,120 ivory tusks, 13 rhino horns and five leopard skins," ports control head Vincent Wong told reporters.
The total weight of the goods was 2,266 kilogrammes (2.27 metric tonnes) with an estimated value of about HK$41 million ($5.29 million), Wong said, adding that the shipment had passed through Shanghai.
"I think Hong Kong is not the final destination. The items can be temporarily stored in Hong Kong and then when there is a buyer who can afford it, the smugglers can smuggle the goods to them," Wong said at the press conference where the seized goods were displayed for reporters.
No arrests were made, but anyone found guilty of trading of endangered species for commercial purposes are liable to a maximum fine of HK$5 million and imprisonment for two years.
Last month, more than 1,000 ivory tusks, mainly from baby elephants, were seized by the city's customs.
Ivory is popular with Chinese collectors who see it as a valuable investment and leopard skin is a popular material for fashion and decoration.
Products made from the endangered rhinocerous are popular in the Asian market, where their horns are believed to have medicinal properties -- such as curing cancer -- despite the fact that no scientific evidence exists to support such claims.
Hong Kong, a free port which runs one of the biggest container terminals in the world, often sees the seizure of products from banned trades.
But customs officials have previously said there was "no concrete information" to show that the financial hub had become a gateway for ivory smuggling.