Photos taken by police showed writhing lizards piled on top of each other in small plastic bins filled with soiled pellets.
Another photo showed a snake curling around a clutch of eggs in a clear plastic tub packed with wood chips.
Each lizard could fetch as much as A$5,000 (US$3,360) on the black market, police said, giving the total seized haul a street value of as much as A$1.2 million.
Police have charged three men allegedly involved in the “criminal syndicate” – aged 59, 54, and 31 – as well as a 41-year-old woman.
Hong Kong is a major global transit point for the illegal trade in live animals, according to the World Wildlife Fund.