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ISLAMABAD, Dec 16 — In a country that has more than 20,000 religious schools, Pakistani investigators say the madrassa where Tashfeen Malik studied the Koran doesn’t stand out as being especially radical or linked to past violence.

But experts here can’t say the same about every other madrassa in the country. Religious schools provide Koranic teachings to 3.5 million children and young adults in Pakistan, and officials and analysts think that a small but significant number of these institutions act as incubators of radicalism.

Malik’s killing of 14 people in San Bernardino, Calif. — in an act carried out with her husband — has refocused attention on the roots of Islamist extremism here.

The Al-Huda Institute, where Malik studied, is relatively obscure and not known for being confrontational, although four female students at its affiliate in Ontario did leave Canada to try to join the Islamic State, the Canadian Broadcasting Corp. reported.

But observers trace some of the strong currents of religious radicalism in Pakistan back to similar institutions. Critics argue that the government has fallen short on its promise to police the madrassas and that the most extreme among these institutions have allowed a radical and violent view of Islam to grow here, even beyond their walls.

If Malik was radicalized in Pakistan, it was because she was exposed to ways of thinking that these schools have helped to promote.

“They require people to isolate themselves from modernity — television is wrong, eating McDonald’s is wrong, mixing with [the] opposite gender is wrong,” said Mosharraf Zaidi, an Islamabad-based columnist who specializes in education issues. “And once you establish that isolation, then dehumanizing people is easy . . . and if you leave someone there, you have left them on a cliff.”

Wednesday was the first anniversary of a Taliban attack on a school in Peshawar that killed more than 150 teachers and students. The attack galvanized the government and public around a significant military response as well as reforms to clamp down on extremist views. Madrassas were not excluded.

In January, the government released a 20-point action plan, which included the “registrations and regulation of madrassas.” But even though much of the plan is now being implemented — helping to reduce the number of terrorist attacks in Pakistan this year — the government remains conflicted over how aggressively it should, and can, confront the country’s powerful network of Islamic religious leaders and teachers.

With Islamic study a key characteristic of Pakistani society, government officials say they are struggling to differentiate legitimate faith-based teachings from those that spew intolerance or actively recruit militants.

“Only a few madrassas can be dubbed as fomenting extremism, which nurture terrorism,” said one senior Interior Ministry official, who spoke on the condition of anonymity to discuss the matter freely. “Muslims go to mosques and madrassas to pray and for religious education, and they send their children, too, but that doesn’t mean they are getting radicalized.”

Yet many security analysts are far more pessimistic about the nature of the threat.

Muhammad Amir Rana, a terrorism expert who helped draft the government’s response to the Peshawar school attack, said madrassas pose a “very serious threat” because they set their own criteria for who or what should be considered “enemies of Islam.”

“Terrorism has different shades,” Rana said, “but madrassas have been the nursery.”

Abdul Hameed Nayyar, a retired Pakistani physics professor who has extensively studied madrassas, said even moderate Islamic schools mix religion with politics and spend considerable time on topics such as jihad.

“They teach this kind of anger, an anger that many perhaps keep under control but others are not able to keep control over, and that anger comes out in the form of jihad,” Nayyar said.

Although Pakistan’s religious seminaries predate the country’s founding in 1947, the numbers grew significantly during the 1980s.

At that time, the United States and Saudi Arabia were pouring money into religious education in Pakistan in support of the Muslim rebels resisting the Soviet invasion of neighboring Afghanistan. Later, in the 1990s, some madrassas served as pipelines for militants associated with Pakistani-backed insurgents in Indian-ruled Kashmir.

It wasn’t until after the terrorist attacks of Sept. 11, 2001, that Pakistani madrassas became a major source of international concern. In response, Pakistan began assessing how many madrassas had opened here over the previous three decades.

Today 26,000 madrassas are registered with an umbrella organization, Ittehad-e-Tanzeemat-e-Madaris. Some Interior Ministry officials think that 9,000 others may be unregistered.

One ministry official estimated that 2 to 3 percent of Pakistan’s madrassas can be linked to the radicalization of students. Over the past year, the government has closed about 100 of these over suspected links to militancy.

Nayyar, however, estimates that 5 percent of Pakistan’s madrassas “are very active in jihad.” An additional 20 percent to 25 percent, he said, stand ready to provide logistical support to groups engaged in armed conflict.

“It is this collection that could be there for jihadis if there is a need,” Nayyar said. “They could be given places to hide and be the ones actually taking care of jihadists.”

On a recent visit to a madrassa in Mardan, in Pakistan’s northwestern Khyber Pakhtunkhwa province, both students and administrators seemed well aware that their way of life is under heightened scrutiny.

The Darul Uloom-e-Islamia al-Arabia madrassa has 1,400 students, about 600 of whom live on-site for round-the-clock exposure to religious education.

The madrassa is affiliated with the Deobandi sect of Sunni Islam, from which groups such as the Taliban have historically found their greatest sources of support.

“There is common perception that madrassas are a hub of terrorists and they are giving terrorists training, but I don’t even know how to use a pistol,” said Ijazullah Khan, 24, a seventh-year student. “It’s just been my childhood desire to join religious school and get Islamic education.”

Maulana Tayyab, the administrator, also recoils at suggestions that madrassas fuel terrorism.

Still, Tayyab concedes, three of his students were recently arrested on suspicion that they had links to terrorist groups.

“We have a clear policy that we will not support anyone arrested or found involved in terrorism,” Tayyab said. “We disown them.”

Yet Tayyab’s definition of terrorism may not match the Western interpretations of the word.

“The fight between right and wrong is continuing,” he said. “How can we stop teaching jihad, as it is mentioned in the holy book?

“These madrassas have a history of fighting against the British in India, and the [Soviet Union] was defeated by these students and teachers,” Tayyab continued. “Now the U.S. and West feel threatened by madrassas, but we will protect ourselves.”

For Pakistani leaders, trying to evaluate the diversity of teachings in the schools, while assessing the threat that any one school may pose, isn’t easy.

After the Peshawar school massacre, the government asked madrassas to submit information on their sources of funding, spending practices, and the identities of all students and teachers.

But many of the madrassa leaders resisted, saying the process was intrusive and harassing. The data collection was suspended in September, said Mufti Muhammad Israr, a religious scholar who runs a madrassa in northwestern Pakistan.

In recent weeks, there also have been signs of an emerging split between Prime Minister Nawaz Sharif’s government and the Pakistani military over the issue.

In early November, the army’s chief spokesman issued a series of tweets that questioned the government’s commitment to implementing the national action plan.

One security official, who spoke on the condition of anonymity because he was not authorized to talk to the media, said frustrations over the lack of serious madrassa reform are feeding the military’s unease.

“It has to be done by the Interior Ministry, and it can’t be halfhearted,” the official said. “But they are afraid because they think there will be a backlash. They are afraid of the mullahs.”

When it comes to madrassas, said Zaidi, the columnist, “the genie is so far out of the bottle, any real attempt to be assertive is going to backfire.” He noted that Pakistan’s own laws are infused with some of the same Islamic principles taught in madrassas.

“This forces people to confront elements of their own values and belief system,” Zaidi said. “You have a conservative Muslim walking up to an extremely conservative Muslim saying, ‘Hey, this is too much.’ But the way the state has also defined itself as Muslim, and all laws are supposed to be Muslim — that makes it very difficult.”

Haq Nawaz in Mardan, Pakistan, and Shaiq Hussain and Zahid Gishkori in Islamabad contributed to this report