If you care about children’s development and combating extremism, this is a story that should alarm you. A teacher at a London state school largely catering for Muslim girls runs an activity each week: pupils suggest items in the news to talk about, and the class has a discussion. But a week after the Charlie Hebdo atrocity, nobody brought it up. When the teacher spoke to students, she found out why: “Our mothers told us, ‘Don’t talk about that – they’ll put us on a register.’”

The teacher in the story didn’t think any of her students would have said they supported the terrorists, but thought some students might have said drawing the prophet Muhammad should be illegal; others might have felt less strongly. But the opportunity to have the discussion was lost because these pupils thought they would be criminalised.

It’s a story recounted to me by Kevin Courtney, the National Union of Teachers’ deputy general secretary, which sums up fears many teachers have about this government’s approach. Under legislation that came into force this week schools are obliged to have “due regard to the need to prevent people from being drawn into terrorism”. A teacher’s position depends on trust as well as respect. Both could be undermined if teachers are transformed into de facto adjuncts of the police. Pupils could be left feeling they are under even more suspicion than they already are – worse, that they are being spied on. Discussions related to extremism, radicalisation and terrorism could be shut down.

Once again the British state is helping build the sort of extremism it is publicly combating

Even before the despicable massacre of sunbathing tourists in Tunisia, few would have questioned the need for a strategy to deal with radicalisation. Of course it is the responsibility of teachers to report suspicions of students being groomed by Isis and other jihadis, just as is the case with suspicions of grooming for sexual abuse. But making Muslims feel like a fifth column, a potential enemy within, from childhood onwards: this is guaranteed to make British Muslims feel even more besieged and defensive. According to a poll in April, a third of Britain’s Muslim population reported feeling under more suspicion in the past few years.

Given that the research also suggested over half of non-Muslim Britons felt Islam was incompatible with British values, you can see why. British Muslims – a diverse group ranging from those of Indonesian, Turkish, Nigerian, Indian and Bangladeshi descent to white converts – are increasingly regarded as synonymous with terrorism and extremism in modern Britain.

According to the education secretary, Nicky Morgan, homophobia could be investigated as a sign of extremism. As a gay man, I want homophobia to be taken seriously, and think children should be educated about prejudice as early as is feasible. But negative views about LGBT people will not be confronted if children shut down any discussion out of fear of being labelled a potential terrorist. Morgan herself originally opposed and voted against equal marriage: could those much younger than her come under suspicion if they are Muslims?

The teacher at the above school thought some of her pupils might believe drawing their prophet should be criminalised. For those who seize on this as proof of the illiberalism of Muslims, it’s worth noting that a desire to implement state bans on forms of expression that offend is hardly specific to any faith group. According to a poll a few years ago, 82% of Britons wanted to prosecute those who burn poppies, for example. Ideally, education should encourage children to be critical thinkers, able to question whether such crackdowns on free expression are dangerous in a democracy.

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Once again, it is difficult to avoid the conclusion that British state policy is helping to build the sort of extremism it is publicly committed to combating. The former Tory minister Lady Warsi has warned that a policy of disengagement with Muslim organisations has had exactly this counterproductive consequence. Isis and other jihadis want Muslims to feel pariahs in their society, to be the targets of fear and suspicion.

We’ve had 14 years of the “war on terror”, both at home and abroad: the results speak for themselves. The genuinely far-reaching debate we have so far been denied is surely overdue: how about an independent public inquiry into modern extremism? Reducing the phenomenon to any single factor is facile: all must be examined.

How can the British government best engage with and involve its Muslim citizens, and combat a sense of siege? Who is susceptible to radicalisation and why? How much has western foreign policy contributed, as the ex-MI5 head Eliza Manningham-Buller has said it has? What threat is posed by the destruction of both Iraq and Libya? What pressure can the west exert on its own allies – namely Saudi Arabia, Qatar and Kuwait – to stop the export of extremism across the Middle East and beyond?

Defenders of the government often suggest that its critics believe western foreign policy alone is at the heart of radicalisation. The reason for it is undoubtedly a complex interaction of different factors. My fear is that current government policy will seal the mouths of Muslim pupils, leaving them feeling unable to open up for fear of the consequences: a satisfactory outcome for extremists, and nobody else.