Two others escaped after the dramatic chase before dawn last week, she said.About 600 cobras, which were believed to be on the way from southeast Asia to dinner tables in mainland China, are now in the care of the Agriculture, Fisheries and Conservation Department.
Smuggling of exotic animals for food to China is common and snakes are a popular delicacy, especially in winter.
Marine police sighted the mainland Chinese man and two other accomplices in a speedboat heading towards southern China and gave chase.
"During the chase, the smugglers hurled some boxes of cobras at the police vessel and some of the snakes fell into the sea," the police spokeswoman said.
"Both vessels later collided and one of the smugglers fell into the water. When police were trying to rescue him, the other two jumped into the sea and swam towards a (waiting) Chinese vessel just across the border," she added.
The man died from internal bleeding, caused possibly by impact from the collision, she said.
Police searched the smugglers' ship and found 27 boxes filled with cobras, which they said were worth around HK$200,000 (US$26,000).
Cobras are declared endangered in Hong Kong and importing or exporting such species without a permit carries a maximum penalty of a year's imprisonment and a HK$500,000 fine.