Indonesia passed vast changes in legislation redesigning the national scene of counter-terrorism by increasing the role of the military inside the country. Under President Prabowo Subianto, the Tentara Nasional Indonesia (TNI) is now officially permitted to participate in civilian counter-terrorism missions—a major shift from the post-2004 policy that limited the military’s internal involvement after decades of dominance during Suharto’s New Order.
Typical of the situation until this change was to leave matters of counter-terror to a certain extent in the portfolio of the National Police via specialized forces like Detachment 88 (Densus 88) and the National Counterterrorism Agency (BNPT). The agencies recorded significant success, breaking the networks of terrorism such as the Jemaah Islamiyah and arresting the high-profile members. Nonetheless, the changing nature of threats, limiting resources, and the pressures of high operations have stretched them to the limit and thus they have been subject to reforms in 2025, giving the military the mandate to lead or at least assist in missions against the threat of domestic terrorism.
Some critics fear that this reform will reintroduce strains of the so-called dual-function doctrine long since discredited and abandoned that gave the military broad powers to regulate civilian life. There is a lot of concern regarding the issue of excess which is not surprising considering the fact that these new roles were implemented without much consultation of the masses.
Coordinated military-police operations and tactical shifts
Re-emergence of the military in terms of counter-terrorism is based on years of growing collaboration with the police. This incorporates earlier collaborative endeavors including the Operation Madago Raya in Central Sulawesi, a process designed to destroy MIT associated jihadists in confined mountains that police would not be able to access on their own. Its extensive territorial coverage, down to the village level with Babinsa officers gives the military intelligencing gathering capabilities that are very specific to ensuring that the country, with its widely spread geography is covered.
The Special Operations Command (Koopsus) units have proved to be ready in delivery of specific high-risk operations. The fact they were deployed in Papua and Sulawesi regions highlights how joint kinetic interventions are now being implemented and the kinetic response of the military providing logistical power and the immediate use of force complements the intelligence-based approach by the use of police.
Institutional overlap and tensions
With these tactical advantages the shift generates strains with the TNI and the police forces. Terrorism in Indonesia is still considered as a criminal issue thus traditionally investigated and prosecuted by the law enforcement agencies and within the civil courts. The burden of war on the military escalates the need of jurisdiction to avoid duplication of roles and competition in the exploitation of resources. The people will also observe that the structures of military disciplines are completely different from police investigative processes and this poses operational and legal challenges in coordination.
Security analysts warn of potential friction in chains of command, especially where accountability mechanisms are weak. The concern is not only about operational duplication but also the erosion of reforms that ensured civilian primacy in internal security following Indonesia’s democratic transition.
National security priorities and regional alignment
Counter-terrorism presents a larger theme: the reorientation of Indonesia defense policy under Prabowo. Early 2025 announcements to expand regional military commands to 22 rather than 15 imply that an aspiration to tighten coverage of internal threats combined with augmenting strategic containment in tense areas, such as the Natuna Islands. The moves are accompanied by heightened tensions in the region, especially in the South China Sea, where Indonesian authorities have launched increased patrols at sea to stop unauthorized Chinese incursions.
Counter-terrorism is an internal and exterior matter in this wider regional context. Preventing transnational terrorist movement, especially across maritime borders, demands a more mobile and flexible security apparatus—roles the military is arguably better equipped to perform than police forces alone.
Global cooperation and modernization
Indonesia’s pivot toward militarized counter-terrorism aligns with expanding defense ties. Military exercises with the United States and Australia increasingly include counter-terrorism scenarios, reflecting converging security interests. These partnerships also deliver training and equipment, fostering interoperability and signaling Indonesia’s desire to professionalize its armed forces within international frameworks.
Defense expert Beni Sukadis notes that such joint training initiatives “enhance coordination and field-level precision,” especially where armed confrontations with well-organized extremist cells require both speed and proportionality. The TNI’s modernization efforts, supported through these partnerships, aim to address past limitations while projecting a credible deterrent.
Rights concerns and civil society reactions
Not all observers view the changes positively. The rapid passage of the March 2025 amendment with little civil society consultation has fueled apprehension. Human rights organizations including KontraS and Human Rights Watch warn that reintroducing the military into internal affairs risks repeating human rights violations common during the New Order. These fears are compounded by Indonesia’s weak oversight mechanisms and the lack of clarity around which agency leads in situations of overlapping authority.
Legal experts have expressed concern that without an independent civilian oversight framework, the re-empowered TNI could operate in legal grey zones, undermining the rule of law. The legacy of military impunity—especially in conflict areas like Aceh and Papua—still looms large in the public memory.
Prabowo’s justification and evolving threats
President Prabowo has framed the reforms as a pragmatic response to shifting threats. In his May 2025 speech before the National Resilience Council, he argued that “contemporary terrorism demands extraordinary coordination and readiness,” adding that the police alone are overstretched. The emergence of ISIS-affiliated groups in Sumatra and East Java, along with increasingly sophisticated bomb-making capabilities among cells, supports his argument for a wider defense role.
Supporters of the amendment contend that increased military involvement does not mean civilian exclusion, but rather a shared security architecture. They point to expanded inter-agency training and planned parliamentary oversight as safeguards. Still, trust in these mechanisms remains low among human rights advocates and university student groups, who have staged nationwide demonstrations.
Long-term goals and policy integration
The expansion of military counter-terrorism powers must be seen in tandem with other national strategies, particularly in soft-power domains. Deradicalization efforts run by the BNPT, mosque-based community engagement, and prison reform are all essential to preventing extremist ideologies from taking root. These non-military components remain underfunded and under-prioritized compared to hard security measures.
According to experts, such effectiveness of the role of TNI is possible only in case it is included in a broader context. Radicalization can not be solved with the use of military force only or the network of recruitment could not be broken. The strategic success must incorporate an appropriate proportion between the kinetic activity and social resilience policies and long-term governance projects. By the middle of 2025, it does not appear that these types of integrations are occurring at the level required to address rising threats.
Military power and democratic resilience
The case of Indonesia is an example that demonstrates a tension between efficiency and democratic responsibility of the evolving counter-terrorism policy. The boosted position of the TNI with Prabowo represents a redistribution of security preferences though invokes old arguments about civil-military equilibrium. As the international support and internal capacities are coming to a bigger and brighter light, the efficiency of these reforms will precondition on the clarity of their implementation and their compliance with the lawful norms.
How successful the introduction of military back into civilian counter-terrorism practices can become will be tested in the next years to come. That might bring Indonesia to take a step back towards a securitized governing model. The issue is not only to win the war on terrorism, but also not to lose the principles of democracy and human rights in the process of winning the fight against terrorism. During Indonesia recalibration, their decisions will provide a wider insight on the mantra of balancing power and accountability during the period of changing threat.
