Johan Meyer, 53, was arrested Thursday and charged a day later with three counts of being in possession of sensitive nuclear-related equipment and of illegally importing and exporting nuclear material.
US officials have linked Meyer's arrest to Pakistani scientist Abdul Qadeer Khan's secret network to help Libya develop an atomic weapons programme.
The father of Pakistan's nuclear program, Khan, confessed in February that he had shared nuclear secrets with Iran, Libya and North Korea, triggering an international effort to track down the scientist's accomplices.
"They have raided his business premises over the weekend as part of their investigation," said Meyer's lawyer, Heinrich Badenhorst.
"They confiscated a number of containers pertaining to their probe," he told AFP, adding that he did not know its contents.
"My client was just as surprised as we were about it," he added.
The Johannesburg-based Afrikaans daily Beeld said 11 large crates were taken from Meyer's business premises in Vanderbijlpark, about 80 kilometres (50 miles) south of Johannesburg on Saturday.
Quoting unnamed sources, the newspaper said South African officials, under the supervision of a team from the Vienna-based International Atomic Energy Agency (IAEA) dismantled what it described as a suspected uranium enrichment plant.
The crates were taken to Pelindaba, west of Pretoria and which was the once the home of South Africa's nuclear weapons programme under apartheid.
The paper said plans and pictures of a uranium enrichment plant were also found on the premises "which possibly showed that Meyer wanted to modernise the plant or make changes to it."
Abdul Minty, chairman of South Africa's Commission for the Non-Proliferation of Weapons of Mass Destruction, said Monday that investigations into Meyer's alleged activities were continuing, and declined to give details of the case.