My daughter started secondary school on 1 September. She was very excited. I wish I could report that she skipped through the gates on her first day, but this is France, and no child skips through school gates in 2016.

Instead she stood in a queue outside the entrance, as one by one she and her new classmates had their satchels searched by a pair of security guards. Not that I'm complaining. In fact if I did have a gripe it was that the security was too light. According to Bernard Cazeneuve, France's interior minister, 50m euros has been provided to tighten security at schools and colleges, and more than 3,000 police reservists were mobilised when French children returned en masse on the first day of September. There were none outside my daughter's front gates, something of a surprise given it's a Catholic school.

In 2012 Mohamed Merah strolled into the playground of a Jewish school in Toulouse and shot dead three children aged 3, 6 and 8. Following the terror attacks in Paris last November, 4,700 police and gendarmes were ordered to guard the 717 Jewish schools in France. But with more than 8,300 private Catholic educational establishments in France there's no way the State can stand guard over each one.

How the Islamists would love to pull off a spectacular in a French school, as they did in Peshawar two years ago, when 140 Pakistani schoolchildren and teachers were massacred. Isis explicitly threatened French schools a fortnight after the Paris attacks last November. In their magazine, Dar al-Islam they described France's schoolteachers as 'the enemies of Allah' and declared that the country's education 'is a means of propaganda used to impose the corrupt way of thought established by the Judeo-masonry'.

If the beach was the ideological battleground this summer in France, with the burkini the latest weapon deployed by the Islamists to test the resolve of the Republic, the war of attrition in the classroom began more than a decade ago. In 2004 the French government passed a bill outlawing the wearing of conspicuous religious symbols in schools and colleges, a 21st-century reinforcement of the Jules Ferry laws of 1882, which established the secular framework of French education. These rules are enforced at my daughter's new school which, while Catholic in name, caters for believers and those pupils, like my daughter, who aren't of the faith. Her religious education involves learning about the history of all religions and the weekly Mass is optional.

The Islamists were outraged with the passing of the 2004 bill, regarding it an Islamophobic measure to prevent pupils wearing headscarves. This was the opening salvo in an increasingly aggressive campaign run by the Islamists in France to undermine the country's secular education. It's no coincidence that this campaign has been accompanied by the rise in popularity of Salafism, the ultra-conservative Islamic ideology that regards France as a 'société mécréante' - a society of unbelievers.

In 2009, former science schoolteacher turned author Jean-Baptiste de Panafieu, produced a report about the infiltration into French schools of creationism. Explaining that a growing number of pupils refused to accept Darwin's Theory of Evolution, he said they were 'principally young Muslims,' adding: 'Many frequent their local Koranic school. For many of these young people it's a matter of an adolescent and political challenge... the battle against evolution has become, in the last decade, a theme of militancy, of anti-secular propaganda for a small minority of fundamentalists.'

The teaching of evolution in French schools is one source of disquiet for Muslims; so are canteens that occasionally serve pork, and lessons on sexuality and equality which in 2014 resulted in the formation of a protest group, led by Farida Belghoul, a French-Algerian activist. 'This subject creates an enormous emotion,' said Nabil Ennasri, from the Collective of French Muslims, 'because it touches on the crucial question of the transmission of values.' Another emotional time for a small number of Muslim schoolchildren were the days following the murder of the Charlie Hebdo cartoonists in January 2015. French schools observed a minute's silence for the dead but there were more than 200 cases of Muslims refusing to comply.

In February this year an undercover report was broadcast on French television about the spread of Islamic conservatism, using a hidden camera to reveal its extent. In one clip a girl, who could be no more than five, explained to her proud family that she had told her teacher: 'You are not the boss. Allah is the boss.' An isolated case of indoctrination? One would like to hope so but a friend who lives in the southern city of Montpellier told me recently that her six-year-old son returned home from school to announce that on the advice of his playground chums he was changing his favourite colour from blue to green. Why? asked his mother. Because green is the colour of Allah. Meanwhile the latest Islamist arrested in France is a 15-year-old boy, detained in Paris over the weekend on suspicion of plotting 'violent action'.

In recent years there has been a surge in the 'déscolarisation' of Muslim children: in other words, home-schooling. In 2010-11, 18,818 children were home-schooled in France, an increase of 54.6 per cent in three years. Catherine Arenou, the centre-right mayor of Chanteloup-les-Vignes in Yvelines admitted in an interview with Le Figaro this April that the motives for the majority of home-schooled children 'are clearly of a religious nature'. Yet local education authorities can only intervene if there's proof that the homeschooling endangers the child.

One need spend only a few minutes on the internet to find blogs that champion the homeschooling in France of Muslim children. One, 'Musulman Productif', a middle-class blog offering advice on everything from healthy eating to managing depression, lists five benefits of home education. One advantage is that 'it allows a lot more time to devote to the study of Islam and the learning of the Koran'; another is that it prevents virtuous children being exposed to 'drugs, alcohol, cigarettes, bullying, [non-halal] food and immoral behaviour'.

For those Muslim parents unable to homeschool their children, there is another solution: enrol their offspring into one of the growing number of private Islamic schools. There are around fifty in France catering for 5,000 pupils. These establishments are legitimate but others are not. In the past fortnight the French authorities have closed down two clandestine Koranic schools, one of which was in Evry, a town south of Paris, with a large Muslim community. Of the 7,500 children of school age in Evry, 500 didn't appear on 1 September for the start of the new academic year.

I returned to my daughter's school last week for a parents' evening. Normally such evenings fill me with dread - uncomfortable chairs and excessive waffle - but not this time. I was anxious to learn what security measures were in place to protect a Catholic school in Paris in 2016.

Once through the security checks the parents assembled in the school hall for the headmaster's welcoming address. A little bit about the history of the college and then down to business. This year, explained the head, there will be terrorist drills each term to complement the fire drills. He had reviewed security arrangements over the summer with police representatives and plans were in place to deal with a variety of 'incidents' should they arise. He and the teaching staff will meet monthly to discuss and review all security measures. In the event of an 'incident' each parent will receive an email alert instructing us where to go. The challenge, said the head, by way of conclusion, was to strike the right balance between educating the children in a safe and healthy environment without intimidating them by turning the school into a fortress,

I agree. Here's to liberté, égalité, securité.

Gavin Mortimer is a writer and historian who lives in Paris