The commission confirmed it has initiated separate investigations against Roche Holding AG (Roche), Pfizer Inc and Aspen Pharmacare Holdings Ltd.
It said in a statement that it has reasons to believe that Roche and its US-based biotechnology company, Genentech Inc have and continue to engage in excessive pricing, price discrimination and exclusionary conduct in the provision of breast cancer medicine in South Africa.
This was of concern to the Commission because breast cancer is the leading form of cancer affecting women in South Africa.
The investigation into Pfizer is because it is the only provider of a lung cancer treatment medication known as xalkori crizotinib in South Africa, which is also unaffordable by patients.
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"The commission also has information that gives rise to a reasonable suspicion that Aspen has and continues to engage in excessive pricing in the provision of certain cancer medicines in the country.
"The commission has identified the healthcare sector, and in particular pharmaceuticals, as a priority sector for its enforcement efforts due to the likely negative impact that anti-competitive conduct in that sector would have on consumers in general and specifically the poor and vulnerable," commissioner Tembinkosi Bonakele said.
Aspen, headquartered in South Africa with operations in 50 countries, and which had earlier been cleared of other anti-competitive allegations, said it had "noted" the commission's announcement and that it was committed to full and constructive engagement in the investigation.
"We await the opportunity to be contacted by the Commission to clarify the pricing for this product," it said in a statement.
Swiss company Roche also said it would co-operate fully with the authorities.