The motorist, a South African man, had 27 black plastic bags containing more than 13,000 of the molluscs, the ministry said.
The bags, weighing 640 kilos (more than 1,410 pounds), were worth more than one million rand ($55,000, 50,000 euros), authorities said.
Poachers loot South Africa's coasts of the highly sought-after sea snail, which is protected by strict fishing quotas.
The ministry called for a "swift prosecution" of the suspect, who was detained last week during a random stop and search by police in the Eastern Cape, a province known for its long, wild Indian Ocean coastline.
"I urge every South African to be vigilant and report any environmental crimes to the authorities," said Deputy Environment Minister Narend Singh.
"It is crucial that our communities work hand in hand with law enforcement agencies to protect our marine resources."
The volume of illegally caught abalone has almost doubled over the past decade, according to wildlife trade monitoring network TRAFFIC.
The once abundant high-end delicacy, a chewy sea snail with a distinctive salty taste, is popular at feasts and wedding banquets in parts of eastern Asia.
Trafficking networks are known to be often run by Chinese criminal syndicates.
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