Anwarul Haq, a frail, bespectacled cleric, sits before a class of attentive students in Darul Uloom Haqqania, one of Pakistan’s many madrassas, or Islamic seminaries. His class of 1,400 students is the most senior of 4,000 enrollees at Darul Uloom, an hour's drive from Peshawar.

The students follow a 500-year-old curriculum adopted across South Asia. The oversized book used in Mr. Haq's class, a collection of ahadith, or sayings attributed to the prophet Muhammad, is centuries old and written in Arabic. Commentary written in Urdu in present-day India fills the margins.

“This country was built on Islam, the idea of following God's teachings. Here we are learning how to do that,” says Haq.

What students learn, and don’t learn, in thousands of such private seminaries is a matter of concern for Pakistan’s government. Under a national security policy unveiled last month, Pakistan aims to bring madrassas under tighter state control, update their curricula to tone down extremist views, and introduce subjects like mathematics and science. The goal is to turn out graduates capable of getting decent jobs who won’t be tempted to join the Taliban or other militant groups.

“Graduates stand in between two worlds,” says Nafisa Shah, a lawmaker from the ruling Pakistan Muslim League. When they don't get jobs, she says, “they become vulnerable [to recruitment by militants].”

Pakistan currently has a tenuous ceasefire with homegrown Taliban militants and has released scores of suspected militants and accomplices in confidence-building measures. Still, terrorist attacks have continued by splinter groups the Taliban claim not to control. On Apr. 9, 21 people were killed in a blast at a fruit market in Islamabad.

Advanced degrees

Fears that Pakistan’s madrassas are breeding grounds for extremism are nothing new. After 9/11, the US government funded a $100 million madrassa reform program that met widespread hostility and failed to make much headway.

Clerics have scoffed at the government’s new security policy and point out that they’ve already instituted the kind of reforms the government advocates. Darul Uloom offers advanced specializations in Islamic law that Pakistan’s universities accept as Master's degrees, and runs computer labs for students.

Other madrassas have also upgraded their curriculum so that students, who spend much of their time memorizing the Quran, get a broader secular education. Most pupils are from poor backgrounds: madrassas offer free education, housing, and food.

Moreover, experts say the threat of militancy comes mostly from what students learn in their spare time, especially in hundreds of underground madrassas that are beyond the reach of both the clerics and the state.

“Most policy makers have never even visited a madrassa,” says Qibla Ayaz, the dean of Islamic and Oriental Studies at Peshawar University, where half the doctoral candidates are graduates of madrassas. By including madrassas in the national security policy, he says it’s clear the government “considers them a law and order issue, a security problem, not an educational problem.”

Taliban admirers

Still, it can be tough to untangle these challenges. At Darul Uloom, it’s not hard to find admirers of the Taliban and its intolerant brand of Islam. In the 1990s, hundreds of students joined its ranks, and some rose to become senior commanders.

The school's faculty, including Haq, still enjoy enough respect among the Taliban that they were nominated by the group's leaders to represent them in the current peace talks.

Haq is the vice president of an independent body of clerics overseeing 1.6 million students enrolled in Pakistan's roughly 18,000 madrassas. He's highly critical of government meddling in the sector, and in particular of the US-funded reform program that ran between 2002 and 2008. Clerics that usually divided along sectarian lines formed an alliance to resist the US-backed reforms and only agreed finally to hand over a list of their madrassas.

“Every government for the last forty years has tried these reforms, we are used to dealing with them,” says Haq. “They are the servants of the US, of infidel governments. They say they want to help, but they really want to erase Islam, and they know madrassas are the final obstacle.”

In Darul Uloom’s computer lab, nearly 350 students use dozens of old desktop computers for classes on how to type, or surf the web. By contrast, only 39 percent of government schools in Pakistan have electricity. Three million children never attend a single class, according to an official 2011 survey. Critics say the focus on regulating madrassas ignores the broader failure of Pakistan's leaders to invest in primary education.

Computer literacy

The school's computer literacy course was started nearly 15 years ago in response to demands by students. Most students also sign up for extra classes in science or mathematics that use the same curriculum taught in government schools, says Haq.

Most graduates from Darul Uloom work as clerics, but hundreds have had successful secular careers. Muneer Alam is among them: he graduated in 2003 with an advanced degree in Islamic law, then went to medical school and became an endocrinologist. He now runs a clinic outside Rawalpindi. “People see Islamic education as an obstacle, but it isn't,” he says.

Ammar Khan Nasir, an expert on modernizing Islamic studies who teaches at Al-Sharia Academy, a university in Gujranwala, says madrassa curricula need to be updated so students understand the modern nation-state. But he warns this alone isn’t enough to staunch the recruitment of militants in war-torn tribal areas near the Afghanistan border.

“They study the same curriculum that was in place 500 years ago," he says. What's changed, he adds, is what they hear in their spare time, a vitriolic narrative that pits the West and the Pakistani state against Islam. [Editor's note: The original version misidentified Mr. Nasir's university and wrongly attributed a direct quote to him.]

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Fakhar Kakakhel, a journalist who reports from the tribal areas, says around a hundred madrassas used to supply militants with child suicide bombers. Set up to help children memorize Islamic texts, these seminaries operated on a shoestring budget and were not registered with any clerical oversight body. [Editor's note: The original version implied that all the madrassas are still active.]

After a decade of war though, Kakahel says parents are starting to pull children out. “They say we sent our kids to learn the Quran, not become suicide bombers.”