The directorate, which reports to the minister, is responsible for regulating so-called radioactive nuclides, used for a variety of medical, scientific, agricultural, industrial and commercial purposes.
Briefing parliament's health portfolio committee, the health department advised MPs that it had lost over 200 radiation filters and was working on tracing them.
Health director-general Precious Matsoso reportedly told the committee that the exact numbers of lost "sources" was uncertain, as the directorate was inadequately staffed and its database has not been properly updated.
Exposure to radioactive nuclides poses a cancer risk.
In a statement, DA MP Mike Waters - a member of the committee - said regulation and control of such sources of radioactive material was in a complete mess, and posed a risk to national security and to public health.
"The DA believes that Health Minister Aaron Motsoaledi should, as a matter of urgency, ensure that an emergency task force is put in place to recover radioactive nuclides which have been lost or stolen.
"The portfolio committee on health was today briefed on the concerning state of the Directorate of Radiation Control, which is responsible for regulating the possession, use, transport, import and export of radioactive nuclides.
Lost at sea, lost in transit or stolen
"During the briefing, it was revealed that there are a large number of lost radioactive nuclides. Some of the radioactive material has been lost at sea, lost in transit or stolen."
Water said the directorate's inaccurate database meant it was not exactly sure how many sources and what kinds of radioactive material had been lost.
It was therefore difficult to properly assess the national security and public health risk.
Sense of urgency
"Although a task team has been created in the Health Department, there is no sense of urgency to recover the lost radioactive material," Waters said.
Contacted for comment, the department could not immediately say what exactly was missing and what further action the ministry planned to take.
Asked what the department planned to do about the missing material, spokesman Fidel Radebe said: "I need to establish what measures will be put in place."
Asked what exactly was missing, and in what quantities, Radebe said the department would respond to these questions later. (Sapa/ November 2010)