Security concerns are escalating in the battle to eliminate ISIS, driven by a threat no less serious than direct military challenges – the potential infiltration of the interim Syrian government’s security and military institutions by ISIS cells. This risk is increasingly viewed as one of the most dangerous factors capable of undermining counter-terrorism efforts, particularly at a time marked by institutional restructuring and the accelerated integration of former armed elements into newly formed state bodies.
As the security landscape grows more complex, with multiple armed groups having been partially or fully integrated into transitional government institutions, serious questions have emerged over the level of vetting that accompanied these processes. Years of prolonged conflict and overlapping local and ideological loyalties have created fertile ground for extremist elements or ISIS sympathisers to slip into security and military ranks, exploiting administrative chaos and the urgent need to fill security vacuums.
Despite losing its former territorial control, ISIS has repositioned itself through sleeper cells and covert networks that rely on infiltration and internal action. Penetrating transitional government security institutions represents a compounded threat, granting the group access to sensitive information, the ability to disrupt military operations, and the capacity to carry out precise attacks at critical moments.
The reconstruction path
Syrian political researcher Abdul Rahman Rabou’, based in Cairo, says the process of rebuilding Syria’s security and military institutions does not appear to be proceeding according to planned frameworks or established standards. He argues that the integration of certain factions and the recruitment of their members fail to meet recognised criteria for institutional merger and enlistment.
Speaking to +963, Rabou’ says that adopted training and rehabilitation programmes have proven ineffective, unable to produce officers and recruits capable of performing their duties professionally. This situation, he adds, is compounded by disorder and mismanagement stemming from limited experience, weak hierarchies, and fragile internal regulations governing discipline and command – all of which negatively affect overall performance and institutional cohesion.
Rabou’ points to clear infiltration by extremist elements into both security and military institutions, attributing this to several factors, foremost among them the integration of former factions and recruitment based on kinship, neighbourhood ties, and mediation. Such practices, he warns, undermine established standards and expose both institutions to devastating risks, opening the door to fragmentation at the first real test.
He adds that 2025 alone has witnessed dozens of incidents reflecting this phenomenon. On the security level, serious crimes have occurred, resulting in the deaths of detainees due to mistreatment in police stations, departments, prisons, and detention centres, alongside violations during raids and security operations.
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Religious disputes
Within the military institution, Rabou’ says the situation is no less alarming. He notes that clashes have occurred inside barracks between new volunteers over religious debates and disagreements, alongside widespread penetration of extremist ideology within certain units. Such dynamics, he warns, could at any moment trigger a repeat of violent episodes like those seen in the coastal region and Suwayda.
Rabou’ believes there is no simple solution to these complex challenges, but argues that activating and strengthening the roles of defected officers – many of whom have been reinstated to security and military positions – could contribute to building institutions that meet national needs. He also stresses the importance of external training programmes conducted abroad in helping establish a professional police force and army.
He emphasises that military and security academies must rise to the responsibility placed upon them by producing sufficiently qualified officers and non-commissioned officers, ensuring the prevention of extremist infiltration and protecting the country from future security threats.
A real threat
International relations and counter-terrorism researcher Sherif Al-Dawakhli warns that infiltration of security and military institutions poses a genuine threat to the transitional government’s efforts to combat ISIS. He says several recent incidents confirm the existence of real breaches within security bodies at this stage.
Al-Dawakhli points to the attack on a joint US–Syrian patrol on 13 December near Palmyra in the heart of the Syrian desert, which killed two Syrian soldiers and two American civilians, and wounded three US troops and two Syrian security personnel. He describes the incident as clear evidence of institutional infiltration.
Speaking to +963, he adds that the danger of the attack was compounded by revelations that the perpetrator was a member of the interim government’s internal security forces, exposing deep flaws in the process of rebuilding security institutions following the dissolution of the former army and the restructuring of security and military bodies based on armed factions, some of which hold hardline religious views.
Al-Dawakhli notes that the infiltration has been exacerbated by what he describes as superficial integration of extremist factions, which retained their organisational structures and ideological frameworks without genuine transformation. The appointment of foreign fighters to leadership positions within security and military institutions has further complicated the situation.
He explains that the Palmyra attack was the first to result in American fatalities since the fall of the Assad regime, and the first since Donald Trump’s return to the White House earlier this year. It also came amid unprecedented US openness towards Damascus and efforts to restructure the Syrian army.
Al-Dawakhli believes the incident will not undermine security and intelligence coordination between Damascus and Washington, but is more likely to strengthen it, given Syria’s current position as a key US ally during its transitional phase.
He concludes that ISIS appears intent on escalating attacks against both government forces and international coalition troops to demonstrate its continued operational capability in areas under Damascus’ control. The group has, he argues, succeeded in infiltrating internal security forces by exploiting the urgent need to expand personnel numbers and the insufficient scrutiny of new recruits’ backgrounds.
Preventing the rebuilding of ISIS influence within security and military institutions, Al-Dawakhli concludes, requires restricting and acting upon existing lists of individuals affiliated with extremist organisations – particularly ISIS – alongside sustained surveillance and monitoring of these elements.
