The drugs, valued at around $50 million (43.7 million euros), were stashed at the bottom of a container ship docked in Ngqura, Lieutenant-General Godfrey Lebeya, head of an elite unit known as the Hawks, told AFP.
The ship had arrived from Brazil and was bound for India via Singapore, he said.
"The drugs were hidden at the bottom floor in the ship, which had over 3,000 containers," he said.
Acting on a tipoff, investigators raided the vessel on Monday afternoon and found 706 bags, each containing a kilo (2.2 pounds) of the narcotic, Lebeya said.