When Covid‑19 struck in early 2020, the government created two emergency bodies to centralise decision‑making: the National Coronavirus Command Council (NCCC) and the National Joint Operational and Intelligence Structure (NatJoints). Intended as temporary crisis‑management tools, one has not formally been repealed, and the other has now become a permanent fixture that operates largely out of public view.
Five years later NatJoints continues to shape policy, security and even electoral processes, raising serious questions about accountability and the future balance of power in South Africa. Five years after the Covid‑19 pandemic forced the government to create an emergency security apparatus, NatJoints continues to operate behind closed doors, shaping the nation’s response to everything from high‑profile political events to whistle‑blower protection.
NatJoints was born in March 2020 under a temporary amendment to the National Security Act, intended to coordinate intelligence, police and defence resources during the health crisis. The amendment was never repealed, and the structure has since morphed into the de‑facto security coordinator for any event deemed “nationally significant.”
In the run‑up to the 2025 State of the Nation Address, NatJoints announced a two‑nautical‑mile no‑fly zone around Cape Town’s City Hall, road closures, and a massive police deployment. The council’s briefing emphasised “meticulous preparation” and “swift action against unlawful behaviour,” echoing the same language used during lockdown enforcement.
The annual Mining Indaba in Cape Town also proceeded “without incident” thanks to NatJoints’ “continuous monitoring” and “strategic meetings” with law‑enforcement agencies. While the conference was praised for its smooth operation, critics note that the same security apparatus that safeguards mining investors could be redirected toward political ends.
Perhaps the most troubling episode involved the Madlanga Commission hearings. After the murder of whistle‑blower “Witness D” – identified as Marius van der Merwe – during the commission’s investigations, NatJoints issued a statement promising “enhanced security” for future hearings. The response focused on physical protection but did not address the broader climate of intimidation that allowed the killing to occur, leaving witnesses and journalists vulnerable.
Accountability gaps surround NatJoints. No official roster of its members has ever been published; the council is said to include senior officials from the Presidency, SAPS and the National Intelligence Agency, but the full list remains undisclosed. Opposition MPs seeking to summon NatJoints officials have been blocked on “national security” grounds, and the Joint Standing Committee on Public Accounts has been denied access to the council’s budget, which is hidden under a generic “Special Projects” line item.
The legal basis for NatJoints is equally murky. The 2020 amendment that created the body was intended as a temporary measure for Covid, yet it was never formally repealed. As a result, NatJoints operates in a legal grey zone with no clear statutory mandate or sunset clause, allowing it to wield significant power without democratic oversight.
Civil‑society groups and opposition parties are now demanding a parliamentary inquiry with subpoena powers to investigate NatJoints’ membership, budget and decision‑making processes. They also call for legislative clarification that either formally disbands the council or codifies its mandate with clear limits and oversight mechanisms, as well as robust whistle‑blower protections that go beyond “enhanced security” statements.
If NatJoints remains unchecked, its shadowy influence could extend further into South Africa’s political and economic life, shaping everything from election logistics to infrastructure projects. Conversely, a transparent legislative framework could preserve the council’s coordination benefits while restoring democratic accountability.
As the 2026 State of the Nation Address approaches, all eyes will be on whether NatJoints continues to operate in the dark, or steps into the light of parliamentary scrutiny.
Mukundi Budeli is a final year LLB student at the University of Witwatersrand and an Associate of the Free Market Foundation.
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