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Policy to Practice: Institutional Capacity Gaps in Uganda's Prevention of Violent Extremism and Terrorism Strategy

A Policy Paper on Institutional Capacity for Preventing and Countering Violent Extremism in Uganda
By Omar Dawood Kalinge-Nnyago, PhD
26 Jul 2026

1. Introduction
Uganda occupies an uneasy position in East Africa's violent extremism landscape. It has not suffered the scale of attacks endured by Kenya, Nigeria or Somalia, but it has experienced enough — the 1998 Kichwamba massacre, the 2010 Kampala bombings during the World Cup finals), the 2021 wave of IED and suicide attacks, and a further attempted, if controversial, suicide bombing on Martyrs Day in June 2025 — to keep violent extremism on the national agenda (Institute for Security Studies, n.d.; The Soufan Center, 2025). In February 2022, the Cabinet approved a National Strategy for Preventing and Countering Violent Extremism and Terrorism, intended to operationalise a Whole-of-Government and Whole-of-Society response consistent with the UN Secretary-General's 2016 Plan of Action to Prevent Violent Extremism (United Nations, 2016). Yet by the end of 2023, the U.S. State Department's annual terrorism report still recorded that the Strategy “had not yet been implemented … owing to disagreement over which agency should lead the effort” (U.S. Department of State, 2024).

This paper draws on three successive rounds of applied field research in which I participated directly as consultant, lead researcher or learning manager: the 2018–2019 Building Resilience in Civil Society (BRICS) study of violent extremism in Eastern Uganda; the 2019–2023 Collective Resilience Against Extremism (CREATE) learning programme implemented by Mercy Corps in Uganda, Kenya and Tanzania; and the October 2025 structural and capacity assessment of four Ministries, Departments and Agencies (MDAs) conducted as the baseline for Mercy Corps' Preventing Extremism through Advocacy, Resilience and Local Action (PEARL) programme. Because portions of this work were undertaken on behalf of client organisations and remain restricted, this paper does not reproduce or quote directly from the underlying reports. It instead synthesizes their findings, in aggregate and in the author's own words, alongside publicly available literature, to argue that Uganda's WoG-WoS commitment on paper has not translated into WoG-WoS capacity on the ground — and that this gap carries real security cost given the ADF's demonstrated resilience across the border in the Democratic Republic of Congo (DRC).

2. Uganda's National PCVE Strategy: Pillars and Institutional Design

Because much of what follows will be unfamiliar to readers outside Uganda's PCVE community, it is worth setting out what the Strategy itself commits government to before assessing whether that commitment has been met. Uganda has been developing its national PCVE Strategy since 2017 under a National Technical Committee (NTC) housed within the Ministry of Internal Affairs (MIA); the draft was validated by stakeholders in August 2019 and adopts a whole-of-society framing built around ten priority areas (Life & Peace Institute [LPI], 2020):

Read together, these ten priorities describe a genuinely whole-of-society ambition: only the first is a pure coordination function; the remainder distribute responsibility for prevention across community engagement, governance, youth, gender, education, communications and the justice system — institutions well beyond the security sector. Operationally, the Strategy names MIA as lead coordinator, houses cross-border early-warning functions under the Cross-Border Early Warning and Response Unit (CEWERU), links to the National Counter-Terrorism Centre (NCTC), and envisions the NTC as the body bringing MDAs and civil society together (Kalinge-Nnyago, 2025).

On paper, the architecture is coherent and consistent with regional frameworks such as IGAD's Conflict Early Warning and Response Network (CEWARN).

The difficulty is not the design; it is the depth of institutionalization behind it. Romaniuk and Durner (2018), writing before the Strategy's validation, warned that PVE programming in Uganda would be shaped by contested interpretations of the threat and a history of strategic rent-seeking behaviour around counter-terrorism assistance — a caution that anticipated exactly the kind of institutional ambiguity later documented on the ground. Independent research into the Strategy's own drafting process found that the NTC overseeing it was, at validation, composed entirely of security and intelligence officials, with no standing civil society representation (LPI, 2020). Four years after Cabinet approval, the Strategy's custodianship is still unresolved between MIA and NCTC (U.S. Department of State, 2024; Kalinge-Nnyago, 2025), and the WoS half of the equation — engagement of non-security ministries, local government and civil society — remains, as this paper shows, structurally under-resourced.

3. Evidence of an Implementation Gap

3.1 Leadership Without Resolution

Across the four MDAs assessed for PEARL in October 2025 — MIA, NCTC, the Amnesty Commission, and the Ministry of Gender, Labour and Social Development (MGLSD) — governance and leadership scored 3.00 out of 5.00, the second-highest of five capacity domains, reflecting a genuine national framework and clear legal mandates (Kalinge-Nnyago, 2025). Yet the same assessment found that the Strategy remains undisseminated, with coordination housed ambiguously between MIA and NCTC — the identical fault line flagged in public reporting since 2022 (U.S. Department of State, 2023, 2024). This is not a new problem restated; it is the same problem, unresolved across three years and two independent lines of evidence — one public, one field-based.

3.2 A Widening Prevention Deficit Outside the Security Sector

The starkest finding across all three research streams is the near-total exclusion of non-security MDAs from PCVE implementation. In the PEARL baseline, MGLSD — the ministry constitutionally responsible for youth, gender and social protection, the very domains most cited in the region's radicalization literature (Africa Center for Strategic Studies, 2022) — scored zero across human resource capacity, programmatic expertise, and resources, the only MDA in the sample with no PCVE training, budget, or tools whatsoever (Kalinge-Nnyago, 2025). This mirrors what the BRICS research found in Bugiri, Mayuge and Namayingo districts: recruitment pathways operating through familial ties, informal religious instruction, and promises of education or work — precisely the terrain of social protection, youth and gender ministries, not security agencies (Kalinge-Nnyago, 2019). A national Rapid Threat Assessment later confirmed the geographic scale of this exposure, identifying nineteen high-risk districts spanning the Rwenzori border region to eastern Uganda (AllAfrica, 2024). A WoS strategy that cannot reach its own social ministries — priorities 5, 6 and 7 above — is not yet whole-of-society in practice.

3.3 Resources: The Commitment Nobody Has Funded

Resources and Implementation was the weakest of all five capacity domains assessed under PEARL, scoring 1.80 out of 5.00, with respondents from MIA and NCTC citing total reliance on donor and project funding and the absence of any dedicated PCVE line under Uganda's Medium-Term Expenditure Framework (Kalinge-Nnyago, 2025). Even the Amnesty Commission, the most operationally mature PCVE-adjacent institution — having processed more than 30,000 reporters under the Amnesty Act through six regional Demobilization and Resettlement Teams — operates on a budget too modest to digitize its own case management (Kalinge-Nnyago, 2025). A Communication Strategy co-developed with Mercy Corps has been finalised but never launched or trained on — priority 9 of the Strategy, still unmet in practice.

The same pattern recurs across CREATE's learning documentation in Uganda: strong technical products, thin domestic financing (Kalinge-Nnyago, 2023). WoG-WoS on a zero-budget line is aspiration, not architecture.

3.4 Strength That Stops at the District Line

The one genuinely strong domain across the evidence base is horizontal collaboration: MDAs, UN agencies, the EU, IGAD and CSOs coordinate reasonably well nationally, scoring 3.60 out of 5.00 in the PEARL assessment — the highest of any domain — through mechanisms such as the NTC and multiple MoUs (Kalinge-Nnyago, 2025; United Nations in Uganda, 2024). What is missing is vertical reach: District Security Committees, Local Councils and community Peace Committees are described as active but not systematically linked to national reporting lines, and civil society organisations remain sidelined from prevention programming specifically, even where they are consulted on response. This is the precise gap that PEARL's own geographic focus on Kasese and Bundibugyo — both DRC border districts — is designed to close, and where the CREATE programme's transnational research also found national-local coordination to be the weakest link in the chain (Kalinge-Nnyago, 2023).

3.5 The Civil Society Factor

Civil society sits at the centre of the Strategy's own whole-of-society ambition, yet is the actor most consistently absent from its implementation. Independent research into the Strategy's drafting found that only around twenty-five civil society and human rights organisations participated in the 2019 validation workshop, out of the hundreds active in Uganda's rights and governance space, and that the NTC overseeing the Strategy was drawn entirely from security and intelligence agencies (LPI, 2020). That same research characterised the strained relationship between government and civil society — particularly organisations working on Muslim marginalisation and access to justice — as the single greatest obstacle to effective P/CVE implementation in Uganda (LPI, 2020).

This pattern held six years later. The PEARL capacity assessment found that while a National Technical Committee bringing together MDAs and CSOs now exists on paper, and coalitions such as the Civil Society Coalition Against Violent Extremism (CISCAVE) are active, civil society organisations remain sidelined specifically from prevention programming even where they are consulted on response (Kalinge-Nnyago, 2025). The BRICS research in Eastern Uganda similarly found that community trust — the resource CSOs are best placed to hold — was undermined by respondents' reports of security-force abuse alongside poverty and ideology as radicalization drivers, meaning a security-led response can itself corrode the WoS relationships the Strategy depends on (Kalinge-Nnyago, 2019). Most Ugandan CSOs working on P/CVE are Muslim organisations operating under high state scrutiny and comparatively low funding (LPI, 2020) — precisely the actors best placed to detect early warning signs of radicalization in mosques, madrasas and at-risk families, and precisely the actors the current architecture engages least.

4. The ADF-DRC Factor: Why the Gap Cannot Wait

These are not abstract shortcomings. The Allied Democratic Forces (ADF) — the group most closely associated with Uganda's worst extremist violence since 1998 — has spent the past several years operating from strongholds in eastern DRC's North Kivu and Ituri provinces as the Islamic State's Central Africa Province affiliate (National Counterterrorism Center, n.d.; CSIS, 2021). Despite a joint Uganda-DRC military campaign, Operation Shujaa, that President Museveni credits with killing more than 560 ADF fighters since December 2021 (Reuters, 2025), the group has proven adaptable rather than defeated. The Soufan Center documented a marked resurgence in ADF violence against civilian congregations in July 2025, including an attack on a Catholic church in Komanda that killed close to forty worshippers, and the International Crisis Group separately reported 72 civilians killed in a single September 2025 raid near Lubero — attacks made possible in part because Congolese forces have been redeployed to counter the unrelated M23 insurgency, leaving the ADF more operating space (International Crisis Group, 2025; The Soufan Center, 2025).

Crucially for Uganda, the ADF has not confined this resurgence to Congolese soil. In June 2025, on Uganda's Martyrs Day, the group attempted a suicide bombing in Kampala — its first attempted attack inside Uganda's borders since 2023 — which the Soufan Center reads as a signal that the ADF “retains cross-border networks and the capacity to operate beyond eastern DRC” (The Soufan Center, 2025).

This is the threat against which Uganda's WoG-WoS capacity gaps must be judged. A security-only response — however well-resourced UPDF operations in the DRC may be — cannot substitute for the prevention side of the strategy: reaching at-risk youth in border districts like Kasese and Bundibugyo before recruiters do, addressing the poverty and perceived security-force abuse that BRICS research found driving radicalization in Eastern Uganda (Kalinge-Nnyago, 2019), and giving MGLSD, local government and civil society the tools the security agencies already have. The ADF's demonstrated ability to regenerate from a degraded position in DRC means that Uganda's prevention deficit is not a planning inconvenience; it is a live vulnerability.

5. Recommendations: Closing the WoG-WoS Gap

Six actions, informed directly by the cumulative evidence, would move Uganda's PCVE architecture from design to functioning practice.

Resolve and launch. The single highest-leverage action available to government is a formal, publicly communicated decision on whether MIA or NCTC leads Strategy implementation, followed by the long-delayed public launch of the Strategy, including a popular, accessible version for district and community use. Every research stream reviewed here identifies this as the fulcrum blocking everything downstream.

Fund it. A dedicated PCVE budget line under the Medium-Term Expenditure Framework, even a modest one, would end total donor dependency and allow MIA, NCTC and MGLSD to plan beyond individual project cycles.

Mainstream MGLSD and local government. A ministry scoring zero on PCVE capacity cannot deliver a Whole-of-Society response to a threat whose drivers — youth unemployment, gender vulnerability, weak social protection — sit squarely within its mandate. Targeted training of trainers for MGLSD, paired with localized PCVE modules for District Security Committees and Local Councils in Kasese and Bundibugyo, would begin to close the vertical gap identified across all three research streams.

Institutionalize civil society representation. The National Technical Committee's composition should be revised to include standing seats for civil society coalitions such as CISCAVE and for the Muslim community-based organisations doing the most sustained early-warning and counter-narrative work — converting consultation into representation, and giving the Strategy's own community-engagement and communications priorities (2 and 9) a delivery partner outside government.

Build the missing M&E and digital backbone. No MDA reviewed maintains a functioning monitoring and evaluation framework or digital case-management system for PCVE, despite years of donor investment in strategy documents. A shared, lightweight dashboard — potentially anchored in the Amnesty Commission's existing reintegration data and CEWERU's early-warning tracking — would let PEARL and successor programmes measure whether the gap identified here is actually closing.

Leverage under-used institutional assets. The Amnesty Commission's two-decade track record processing over 30,000 reporters represents exactly the kind of reintegration expertise a WoS strategy should be building on, yet it remains disconnected from mainstream PCVE programming. Positioning it as technical lead for returnee reintegration, rather than a stand-alone DDRR actor, would convert an existing strength into system-wide capacity.

6. Conclusion

Uganda's PCVE Strategy is not short on ambition, and the people implementing it — from MIA's small PCVE coordination team to MGLSD's overstretched focal officer to the CSOs working under-funded and under-trusted at the community level — are not short on goodwill; the evidence from BRICS, CREATE and PEARL is consistent on that point. What is missing is the unglamorous plumbing of a Whole-of-Government, Whole-of-Society response: a resolved lead agency, a funded budget line, a non-security ministry equipped to act on its own mandate, vertical links from Kampala to Kasese and Bundibugyo, and a civil society sector treated as a standing partner rather than an occasional consultee. The ADF's demonstrated capacity to regenerate in eastern DRC and reach back into Kampala means Uganda does not have the luxury of treating these as gradual, second-term reforms. Three separate rounds of field research over seven years point to the same conclusion: the strategy exists; the state has not yet built the capacity, or the coalition, to run it.

References

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