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In the aftermath of India’s Operation Sindoor on May 7, which targeted militant infrastructure in Pakistan and Pakistan-occupied Kashmir, a familiar cycle of accusations and denials has resumed. Pakistani officials immediately labelled the operation a strike on civilians insisting that places of worship, and religious schools, were among the many targets.
Particular attention has been drawn to Markaz Subhan Allah in Bahawalpur, a facility long known as the headquarters of the Deobandi militant group Jaish-e-Mohammed (JeM).
It was here, notably, that Masood Azhar, the proscribed group’s founder, reappeared in December 2024 after years of purported house arrest, a stark reminder of how Pakistan’s most dangerous extremists often operate with impunity, even when officially designated as threats by the international community.
This narrative may resonate in some quarters of the international community, but it masks a deeper, long-running reality which is that many of Pakistan’s religious seminaries, or madrassas, have long played a central role in incubating violent extremism. While not all madrasas are complicit, thousands have served as ideological and operational feeders for some of the region’s most dangerous militant groups.
The connection between Pakistan’s madrassa network and its decades-old strategy of cultivating proxy groups is well documented. And yet, it remains largely absent from current discourses on terrorism globally. To understand the roots of regional instability and why efforts to counter terrorism often flounder, the international community needs come to terms with this institutional reality.
An Infrastructure of Indoctrination
Since the 1980s, after President General Ziaul Haq thrust Pakistan into the frontline of global jihad against Soviet Communists in Afghanistan with the support of United States and Saudi Arabia, the country’s intelligence services, particularly the Inter-Services Intelligence (ISI), have cultivated relationships with a range of militant groups. As the anti-Soviet jihad in Afghanistan folded in the late 1980s, Pakistani Army, having adopted the doctrine of “strategic depth,” the notion that non-state actors could serve as force multipliers in conflicts with neighboring states, redirected these Afghan Jihad returnees to Kashmir. Moreover, an umbrella of Kashmir-centric anti-India groups, such as Hizbul Mujahideen (HM), Lashkar-e-Toiba (LeT), and Jaish-e-Muhammad (JeM), were created to sustain the insurgency in Kashmir. It is instructive when Former President General Pervez Musharraf acknowledged as much in 2010 admitting how Pakistan had supported militant groups to “pressure India.”
But the more pressing question is how Pakistan’s military and its Inter-Services Intelligence (ISI) continue to sustain such a vast militant ecosystem. The answer lies in the decades-old nexus between militant outfits like Lashkar-e-Taiba and Jaish-e-Mohammed, and a wide network of religious seminaries (madrassas) that serve as sources of both ideological indoctrination and recruitment.
While madrassa system of education is not new to Pakistan, but their explosive growth over the last few decades has altered the country’s educational and religious landscape. From just a few hundred at independence in 1947, their numbers have ballooned to more than 30,000 today, a conservative estimate, with nearly half of these operating without state oversight.
While some offer basic religious instruction, many propagate an austere, puritanical version of Islam, often influenced by Saudi Wahhabism and Deobandi orthodoxy — that fosters sectarian intolerance and glorifies armed struggle. For instance, many of these madrassas, as highlighted by M. W. Malla (2020), have relied on curriculum which emotively glorifies “jihad – Islamic holy war – through vivid imagery for whom alif (A) was meant Allah, be (B) meant Bundook (Gun), jim (J) meant jihad, and ha (Ha) meant hathiyar (arms) and likewise.”
A Pipeline to Militancy
In theory, madrassas are meant to provide education and social support to the underprivileged. However, in case of Pakistan, a significant proportion of these Islamic schools serve as gateways to radicalization. The situation is compounded by lack of governmental oversight. For instance, while the officially registered madrasas, numbering nearly 17500 as per governmental statistics, cater over 2.2 million students, millions more are enrolled in the unregistered ones. Consequently, orphaned and impoverished children, often with no other schooling options, are drawn into a closed system where anti-Western and anti-Hindu narratives are presented as divine truth. Recruitment for jihadist groups often begins in these classrooms.
Incidentally, some of the most prominent Islamic religious seminaries of Pakistan such as Jamia Ashrafia in Lahore, Dar-ul-Uloom Banori Town in Karachi, and Jamia Haqqania Akora Khattak have been repeatedly linked to known extremist organizations. Take the case of Jamia Haqqania, which has been referred to as the “University of Jihad” and its former Vice Chancellor Maulana Samiul Haq as the “Father of Taliban.” Much of the Haqqania network leadership and cadre, which is part of Afghan Taliban, has received their religious training from these institutions with a number of them currently surving in the transitional government of Taliban in Afghanistan.
Even as international pressure has mounted, reform efforts have faltered. It is instructive how Pakistan’s current government quietly abandoned the 2019 requirement for madrassas to register with the Ministry of Education, a modest reform that aimed at bringing religious seminaries under state oversight. The reversal came in December 2024, as part of a political bargain with Jamiat-e-Ulema-e-Islam (Fazl), Deobandi religious party led by Maulana Fazlur Rehman, to secure the party’s support for a constitutional amendment that expanded the powers of the military establishment while curbing the judiciary’s independence. Pakistan’s leaders have often found it easier to co-opt these groups than to challenge them — a compromise that comes at significant cost.
Beyond the Madrassa
The culture of radicalization in Pakistan does not stop at religious schools. State-run public schools often include textbooks that promote intolerance, framing India and the West as existential threats. Clerics like Maulana Abdul Aziz, once the head of Islamabad’s infamous Lal Masjid, openly issue calls to violence. He has faced little accountability despite repeated clashes with the state.
This radical ecosystem is self-reinforcing. With 39 percent of Pakistan’s population living below the poverty line, many families have little choice but to send their children to madrassas that offer free food and shelter. But the pattern is not limited to the poor. In recent years, Pakistan has witnessed recruitment by extremist groups among the educated elite, including medical students and professionals drawn to the ideology of ISIS and its affiliates.
This widening appeal underscores that extremism in Pakistan is not simply a problem of poverty or illiteracy — it is one of systemic indoctrination and strategic tolerance. The madrassas are just the most visible node in a much broader network of radicalization.
The Global Dimension
That Pakistan has managed to sustain this infrastructure with relatively few consequences is, in part, a reflection of international inconsistency. During the U.S.-led war in Afghanistan, Islamabad was seen as a necessary, if difficult, partner. More than $33 billion in U.S. aid flowed into Pakistan post-9/11, even as evidence mounted that its military continued to support insurgent groups like Afghan Taliban, LeT, HM and JeM.
What is more problematic is how China, too, despite vying for the global leadership and having endured terrorism in its Xinjiang province, has largely refrained from pressuring Pakistan. This is being justified by its investment in the China-Pakistan Economic Corridor (CPEC) and its geopolitical competition with India. Moreover, while the state patronage of funding conservative religious education from Gulf countries has gone down, the role of religious groups has continued to foster this ecosystem.
In addition, in terms of global oversight, even the Financial Action Task Force (FATF), the global watchdog on terror financing, has struggled to enforce long-term compliance. Though Pakistan was removed from the FATF’s “grey list” in 2022, much of the underlying infrastructure remains intact.
A Familiar Playbook
The claims that India’s recent strikes targeted civilian infrastructure follow a well-established script. In 2019, following the Balakot airstrikes, it denied that any militant camp had been hit, despite independent verification of the target’s history as a JeM facility.
What makes Operation Sindoor different is not the nature of Pakistan’s response, but the context in which it occurs. Militant violence inside Pakistan has surged, with a 79 percent increase in attacks in 2023 alone. Many of these attacks have been carried out by groups the state once sheltered. The Tehrik-i-Taliban Pakistan (TTP), now re-empowered by the Taliban’s return in Afghanistan, has turned its guns inward.
In effect, Pakistan is now haunted by its own proxies, groups once deployed as strategic assets have grown autonomous and hostile. The madrassas that fed them remain largely untouched, a sign of the state’s reluctance, or inability, to dismantle the very apparatus it helped create.
The Consequences of Denial
The madrassa-militancy nexus is not the only reason for instability in South Asia, but it is a critical one.
As long as Pakistan continues to shield this infrastructure behind religious rhetoric and claims of victimhood, genuine counterterrorism cooperation will remain elusive.
For the international community, the lesson is clear: treating Pakistan as a willing partner while ignoring its internal contradictions only delays the reckoning. Madrassa reform, state accountability, and a broader ideological shift are not just domestic imperatives for Pakistan, but they are regional and global necessities.
Until then, any claims of targeting civilians in strikes like Operation Sindoor must be weighed against a broader, uncomfortable truth: some of the very institutions Pakistan defends as sacred have long functioned as sanctuaries for those who preach and practice violence.
Over the past couple of decades, Pakistan has steadily lost favours it once enjoyed with key allies, including the US, for its incessant instrumentalization of terrorism as state policy. As the post 9/11 world increasingly adopted global norms on no tolerance for terrorism, Pakistan remained stuck in its tactics of viewing militant networks as strategic assets, particularly deployed against India. Embarrassingly exposed time and again, the country currently finds itself amid multiple crises at once, from a precarious economic state to existentially threatening insurgencies, all exacerbated by a severely weakened global standing. This was laid bare during its recent hostilities with India, following the blood-curdling Pahalgam attack of April 22, as countries that have traditionally aligned with Pakistan refused to come to its aid.
Pakistan’s role in the proliferation of global terrorism began with its alliance with the CIA in arming the Afghan Mujahideen against the USSR in the 1980s. However, this policy of using militant proxies for geopolitical ends was soon institutionalized by the Pakistani establishment which then deployed the same tactics to undermine India, and specifically stir up Islamist militancy in Kashmir. Even as it projected itself as a US ally in the global war on terror, it continued to shelter and support radical elements, reflected in its infamous distinction between ‘good Taliban’ and ‘bad Taliban’. The primary reason why it covertly backed the Afghan Taliban was again as to secure an allied Islamist regime in Afghanistan as a counter to India. This could not be concealed for long and the US, frustrated by Pakistan’s duplicitous designs, significantly cut down on its economic and military aid to the country, in addition to distancing itself diplomatically.
On the other hand, the continuous terrorist attacks in India, evidentially linked to Pakistan, such as the 2001 Parliament attack, 2008 Mumbai attacks, 2019 Pulwama attack, among others, tarnished the latter’s global reputation as the epicentre of terrorism. In recent years, even Muslim majority nations such as the Persian Gulf countries, particularly Saudi Arabia and UAE, have shifted their foreign policy rationale from religion and ideology-based alignment with Pakistan to a more forward-looking cooperation based on the imperatives of economic pragmatism, regional stability and security, and the emerging new world order, with India.
Similarly, the Organization of Islamic Countries (OIC) has, in the past few years, demonstrated its respect and willingness to engage with India, much to the distaste of Pakistan. The first and quite heavy blow came when the forum invited India’s then Foreign Minister Sushma Swaraj as a ‘guest of honour’ in its 2019 meeting in Abu Dhabi, despite Pakistan’s objections. The next year, in a departure from its usual stance, the OIC declined to have Kashmir on its agenda, reflecting Pakistan’s deteriorating standing in the forum and India’s increasing global clout. Although amid the recent military escalations between the two neighbours in the wake of the Pahalgam terror attack, the OIC appears to have favoured Pakistan’s narrative on Kashmir, inciting censure from India, it remains questionable how long it is going to last, given Pakistan’s free-falling economic, security and diplomatic situation as well as the organisation’s history of snubbing the country’s requests more often than not.
Destabilizing Pakistan’s strategic calculus and exacerbating its internal crisis is its once intimate ally- the Afghan Taliban. Since returning to power in August 2021, an event that was looked at with much optimism and triumph in Islamabad, the Afghan Taliban have turned sour with their neighbour that accuses them of supporting the Tehreek-e-Taliban Pakistan (TTP) or the Pakistani Taliban. The TTP has recently emerged as the most potent insurgent group within the country, in addition to the Baloch Liberation Army (BLA), launching relentless attacks on security forces and civilians, and increasingly establishing proto-state pockets in Pakistani territory. The loss of the Afghan Taliban as a reliable ally against India despite years of covert and risk-laden backing certainly constitutes an existential setback for Pakistan, made worse by the growing engagement between the Afghan Taliban and India.
The decades of Pakistan’s instrumentalization of terror have left it in a position that it itself finds difficult to get out of. Not only has the sponsorship of terrorism backfired on its own people as it ranks 2nd in the Global Terrorism Index 2025, but the years of neglect of its internal issues has bred insurgencies that have attacked even Chinese workers and projects, jeopardizing its most strategic partnership. As Pakistan suffers from alarming inflation, dropping currency and foreign exchange reserves, and dependence on IMF bailouts and bilateral loans, its internal security crises have not only weakened it politically but also economically by staving off any potential investment.
Therefore, in order to prevent its own unravelling, Pakistan must take stock of the shifting geopolitical landscape wherein nations prioritize stability, economic cooperation, and counter-terrorism over religious or ideological affiliations. Its continued backing of terror has already cost it irreparably, both internally and externally. Unless it radically recalibrates its geopolitical strategy, one that has no space for militant proxies, the future seems grim for the country.
Dr. Mahrang Baloch, the charismatic and fearless leader of the peaceful Baloch civil resistance, has been detained by Pakistani authorities alongside 16 other activists for protesting against the ongoing enforced disappearances in the province. As a key organiser of the Baloch Yakjehti Committee, an organisation that has played a significant role in galvanising grassroots mobilisations demanding state accountability, Baloch faces charges including directing terrorist activities, sedition, and rioting. Despite triggering widespread domestic and international condemnation, the Pakistani authorities remain largely unperturbed in their authoritarian suppression of peaceful Baloch demonstrations. In light of the recent escalation in insurgent attacks within the province, the latest wave of arrests and violent repression of protests can be seen as a deliberate attempt to divert attention from the state’s own failures and shortcomings.
Although the Pakistani state has escalated its efforts to silence Baloch this time, she has been under scrutiny for some time. A surgeon by profession, she has played a pivotal role in fostering the peaceful Baloch movement within a highly perilous environment. At just 32 years old, she has witnessed firsthand the severe abuses that the Pakistani state inflicts upon the Baloch people. In 2009, at the age of 16, her father, Abdul Ghaffar Lango, a labourer and political activist with the Balochistan National Party (BNP), was forcibly disappeared. Two years later, his mutilated body was discovered, showing signs of torture and gunshot wounds. In 2017, Baloch’s brother was also forcibly disappeared. Although he was released three months later following Baloch’s vocal opposition to the authorities, her anger and activism endured, and she has since become the voice of many others who continue to suffer similar fates.
Mahrang Baloch gained widespread recognition during the Baloch Yakjehti Committee’s (BYC) ‘March against Baloch Genocide’ from Turbat to Quetta (the provincial capital) and ultimately to Islamabad, held between December 2023 and January 2024. The catalyst for this long march was the November 2023 killing of 24-year-old tailor Balach Mola Baksh by the Counter Terrorism Department, which falsely characterised the incident as an encounter. His family, claiming he was in state custody at the time of his death, protested at Fida Ahmed Chowk in Turbat with his body for a week, but their efforts yielded no results.
The BYC had originally emerged from the Bramsh Yakjehti Committee, formed in solidarity with and to seek justice for Bramsh, the 4-year-old daughter of Malik Naz, who was allegedly killed by state-backed death squads in May 2020. In response to the ongoing state abuses, including enforced disappearances, fabricated encounters, extrajudicial killings, and torture, the leadership of the Bramsh Yakjehti Committee chose to broaden its scope to address the broader plight of the Baloch people, renaming the organisation as the Baloch Yakjehti Committee. The movement is spearheaded by the mothers, sisters, daughters, and half-widows of those who have fallen victim to these brutal state actions, without any accountability. The BYC has since organised a number of significant demonstrations, mobilising people on an unprecedented scale in the history of the province, including the ‘Baloch Raaji Muchi’ in Gwadar in July 2024 and the ‘Baloch Genocide Remembrance Day’ in Dalbandin in January 2025.
In response to the rise of peaceful civil resistance by the Baloch people, the Pakistani establishment, rather than addressing the long-standing grievances of the populace, has resorted to its usual tactics of obstructing, discrediting, and silencing the movement. The protests have continued despite state-enforced internet and network blackouts, arbitrary detentions, the use of water cannons, tear gas, and even live ammunition. Additionally, the state has launched an extensive disinformation campaign against the movement. The mainstream media, traditionally aligned with state narratives, has been complicit in linking the activists to insurgents, alleging that they are supported or manipulated by foreign entities. Dr Mahrang Baloch herself has been targeted by malicious digital propaganda, with false claims that her father and brother were associated with insurgents. Furthermore, an image of her with a Norwegian journalist who interviewed her was circulated, suggesting foreign involvement in the movement. A fabricated audio recording was also spread, falsely claiming that Baloch was attempting to secure foreign funds for the Gwadar protest. A recurring element of the disinformation campaign involves misrepresenting the missing persons, whom the movement advocates for, as separatist militants. In one instance, a photograph of Baloch at a protest was altered to distort an image of a missing person on a poster behind her, replacing the image of Rafique Oman with that of Rafiq Bizenjo, a suicide bomber allegedly claimed by the Balochistan Liberation Army (BLA).
The province of Balochistan has endured immense deprivation and suffering due to the ongoing conflict between the Pakistani state and the long-standing armed insurgency. In addition to the systemic discrimination and exploitation imposed by the federal government, the Baloch people have faced relentless human rights violations by the state under the guise of counter-insurgency measures. The recent train hijacking and Noshki attack on security personnel by the Balochistan Liberation Army (BLA) highlight the complete failure of Pakistan’s policies to address the insurgency and safeguard the Baloch population. Rather than confronting the fundamental issues surrounding its approach, the establishment has reverted to its familiar and convenient tactic of suppressing peaceful dissent to avoid addressing difficult questions.
Dr Mahrang Baloch is currently being held in Quetta District Jail without any legal proceedings, denied access to her lawyer and family. Her cousin, Asma Baloch, has reported that the authorities are even preventing her family from delivering food and other necessary items to her. International human rights organisations, including Amnesty International and Front Line Defenders, have raised concerns about this situation and called for her immediate release. It is evident that the state’s attempt to silence a prominent figure of the peaceful Baloch resistance has backfired, drawing greater attention to the plight of the Baloch people. It is crucial that the establishment reassesses its approach and puts an end to the egregious practices that have fuelled the insurgency and caused immense suffering to the Baloch population.