The South African Council for the Non-Proliferation of Weapons of Mass Destruction said the containers were now stored at a safe location and had been sealed by both South African police and the International Atomic Energy Agency (IAEA) and the two agencies would maintain control.
"IAEA inspectors will visit South Africa on a regular basis to inspect nuclear material and related equipment," the council said in a statement.
It was the first detailed description of the raid last week by police and other investigators on a small engineering firm that led to charges against 53-year-old Johan Andries Muller Meyer for manufacturing nuclear-related material and exporting goods that could be used to develop nuclear weapons.
"At the premises of Tradefin Engineering, 11 shipping containers were found containing components of a centrifuge uranium enrichment plant as well as related documentation," the council said. "Investigations are still ongoing."
Meyer was remanded in custody until Wednesday when his bail hearing will be heard.
Last week the United States embassy in Pretoria issued a statement linking him to Libya's nuclear program, which the north African country disclosed in December 2003 before agreeing earlier this year to a disarmament process.
Libya began its quest for nuclear arms in 1980 and decided in 1997 to seek centrifuge equipment via the atomic black market, established in the 1980s by Abdul Qadeer Khan, the father of Pakistan's nuclear bomb.
Meyer was accused of offences between 2000 and 2001 relating to the import and export of a flow-forming lathe without necessary permits. He was also charged with possessing and producing certain components of a centrifuge enrichment plant without authorization from the minerals and energy minister.
In court papers, Meyer was also accused of "unlawfully and wilfully possessing and manufacturing nuclear-related equipment and material" between 2002 and 2004.
"These items do not constitute a weapons of mass destruction, but they are essential components in the process to enrich uranium," the council said.
Meyer denies the charges, which could result in anything from a fine to a 15-year jail sentence.
Government officials have said they knew of no link between the inquiry and al Qaeda or international terrorism.
South Africa voluntarily dismantled its nuclear arms before apartheid ended in 1994 — the only nuclear-armed state to do so — and has been eager to show support for international efforts to limit nuclear know-how with a series of new laws since 1993.
Khan's network spanned the globe and included suppliers, often unwitting, from Europe, Africa, the Middle East, and Asia.
U.N. atomic weapons experts say more than 20 countries were involved, though it is trying to grasp the full extent of what IAEA calls a global supermarket for countries interesting in acquiring nuclear weapons.