"We will oppose the matter," said Health Department spokesperson Joe Maila.
The Health Products Association of SA, which represents 114 companies producing complementary medicines with an estimated turnover of R7bn, approached the North Gauteng High Court in Pretoria about new government regulations.
The association deemed the regulations "inappropriate" and suggested that they could wipe 60% of their products off the shelf.
However, Mandisa Hela, registrar at the medicine controls council, told the newspaper that if the market was unregulated, it made it "possible to market unsafe products or products of doubtful efficacy".
In the past, complementary medicines were not subject to as strict regulations as orthodox medicine.
However in November last year, new regulations were gazetted that sought proof the medicines were safe and had benefits.
Hela said that in the past, certain products labels did not disclose "unsafe" substances such as yohimbine, teas containing cocaine, and slimming products with dangerous levels of scheduled ingredients.