Gerhard Wisser, 66 a German national and Daniel Geiges, 65, from Switzerland, were arrested on September 8 in South Africa and charged with four counts of contravening the Nuclear Energy Act and a law banning the proliferation of weapons of mass destruction.
"The chamber took the view of the state that my clients represent a flight risk," lawyer Claudia Privato told AFP.
Privato said the judge also found that the release of the two men "could interfere with state witnesses and documents", adding that she planned to launch an urgent appeal to the Pretoria high court to obtain the release on bail of the two businessmen who are living permanently in South Africa.
Prosecutor Chris Macadam said a new hearing was set for November 12.
South Africa is currently investigating ties with a nuclear smuggling network thought to be linked to Pakistani scientist Abdul Qadeer Khan who admitted in February to helping Libya and other nations develop their weapons programme.
South African businessman Johan Meyer was charged earlier this month with possessing sensitive nuclear-related equipment but the charges were abruptly dropped amid widespread speculation that he had turned state witness in exchange for immunity.
A week later, Wisser and Geiges were arrested.
Libya announced late last year that it was abandoning attempts to develop nuclear, biological and chemical weapons after months of secret negotiations with London and Washington.