This article has been updated to correct the spelling of Amsterdam Mayor Femke Halsema's name.

There are two Islamic middle schools in the Netherlands.

One of them has terror ties.

This, at least, was the conclusion of the Dutch intelligence and counterterrorism agencies in March, as described in a confidential letter to Amsterdam Mayor Femke Halsema. Based on an anonymous tip from a moderate Muslim group, the agencies warned that the city's Cornelius Haga Lyceum had "anti-democratic," Salafist leanings. Moreover, the agencies alleged, the school's directors had connections with the Caucasus Emirate, a Chechen jihadist group with ties to the Islamic State.

"Certain administrators would like to devote half the curriculum to Salafistic doctrine," Pieter-Jaap Aalsberg, director of Dutch anti-terrorism agency NCTV, wrote. "They also plan to bring the children into their spheres of influence outside of regular school hours." The goal, it would seem, would be not unlike that of the ISIS leaders: to create a new, young generation of extremists.

This is precisely what the NCTV warned of in its latest report on the terror threat, published in February. "Political Salafists in particular are increasingly teaching an anti-democratic interpretation of Salafist doctrines with the aim of strengthening the 'Islamic identity' of Muslim youth and making their form of Sharia law the guideline for the daily lives of Muslims in the Netherlands," the report stated. "In this way, these political Salafists strive for an autonomous community in which anti-democratic views and behaviors are commonplace. Within the Salafist movement, political Salafists are most actively striving for a replacement, alternative society structure that cannot be reconciled with Dutch democratization."

And how better than to begin in the schools?

Yet current laws make it impossible for the government to remedy the issue without potentially making matters worse. Closing the school down would likely anger the Muslim community and create difficulties for Muslim parents seeking to educate their children in keeping with their beliefs. Meantime, while they grapple with the situation, tensions between Muslims and the government, and between moderate and extremist Muslim communities, are intensifying.

Some of those conflicts were evident in the statement that first alerted the authorities, which was issued via WhatsApp. Describing themselves as "Muslims against Salafism and extremism," the group stated that the school's founders and directors, the brothers Soner and Son Tekin Atasoy, were operating behind the backs of the children's parents and the government, seeking to "indoctrinate young Muslims, with the aim of creating confrontations with Dutch society, and recruiting youth for new rising conflicts elsewhere in the world."

In addition, according to the group's statement, a number of other radicals had infiltrated the school, including Arnoud van Doorn, a former leading member of anti-Islam party Partij Voor de Vrijheid (PVV) who converted to Islam in 2013. Van Doorn has been entirely clear about his views, particularly on Twitter, where he has posted "May Allah destroy the Zionists," and "May Allah guide or destroy the enemies of Islam."

On Monday, he also posted a photo of the school's Ramadan greeting on his social media account.

To make matters worse, when inspectors attempted to visit the Cornelius Haga school in March, administrators abruptly canceled a religion class without offering a reason. According to the NRC Handelblad, which broke the story, a second inspection effort was "made impossible" by the school's directors.

In response, Mayor Halsema immediately halted all public funding of the school, demanded full cooperation with inspectors, and called for Tekin Atasoy to step down as director. But Atasoy refused, setting off a national controversy. While Parliament argued for the forced closing of the school, seeking ways around current laws to do so, radical imams placed videos in support of the school on social media. Cornelius Haga students wrote an open letter to King Willem-Alexander asking if it is his "royal wish for Muslims to be filthied with mud for no cause."

The problem is not limited to Amsterdam. The school is already planning expansion into other cities, leaving officials to grapple with the conflicts between their concerns about the school and the Dutch constitution, which guarantees education to all "with respect for every person's religion or belief" and freedom within special religious schools "with regard to the choice of teaching materials and the appointment of teachers." Moreover, on average, students at Islamic schools score higher than other students on national tests. At the same time, indoctrinating children in radical and violent ideologies is a clear threat to national security.

Hence the dilemma: if the government continues to allow the school to operate and provides funding, it helps feed the Salafist and jihadist narrative. But if it stops, schools like this will likely turn elsewhere for support as mosques throughout Europe have in the past – to Saudi Arabia and Kuwait, for instance – who then install their own extremist directors, imams, and curricula instead.

Meantime, the NCTV has warned that the Islamic State's fall has brought on a "new phase" in Islamic extremist strategy, with an emphasis on recruitment and propaganda, by "setting up new educational and educational initiatives" that will enable them to "dominate non-regular Islamic education." To achieve these goals, the NCTV said, "They successfully raise funds at home and abroad with which they finance these new projects."

Consequently, counterterrorists must also adopt new strategies, including a broader understanding of "jihad." As terror expert Jelle van Buuren of Leiden University told Dutch newspaper Telegraaf, "When we used to talk about jihad, we were always fixated on bombs and Kalashnikovs. Now, we find ourselves looking more at intolerance, and the spread of ideologies. The problem is: if you arrest someone with a Kalashnikov, it's basic. But what do you do with clubs that use democratic rights to undermine democratic values?"

Abigail R. Esman, the author, most recently, of Radical State: How Jihad Is Winning Over Democracy in the West (Praeger, 2010), is a freelance writer based in New York and the Netherlands Her next book, on domestic abuse and terrorism, will be published by Potomac Books. Follow her at @radicalstates.