The nine high-impact sectors identified by the CSIR to achieve its aims are: Industry advancement clusters Industry and society enabling clusters In 1999, a strategic alliance, the Southern Education and Research Alliance (SERA), was formed between the University of Pretoria and the CSIR.

[6] SERA collaborates locally and internationally with universities, NGOs, companies, and multinational bodies in various research areas.

[7] In July 2016, the amaBhungane Centre for Investigative Journalism published an article that alleges that South Africa's Science and Technology Minister Naledi Pandor and Director-General Phil Mjwara were attempting to put undue pressure on the CSIR, at the behest of the African National Congress (ANC) treasurer-general Zweli Mkhize, to favour the Chinese multinational Huawei Technologies in the purchase of a new 116 million South African rand (US$8 million) supercomputer for the institute.

This followed the publication of the council's long-time CEO, Sibusiso Sibisi's, open letter of resignation stating that irregularities and political pressure on the awarding of contracts to suppliers were of great concern.

[8] In a case of biopiracy, bioprospectors from CSIR became interested in the Hoodia plant as an appetite suppressant for weight loss after a marketing campaign falsely claimed its efficacy.