Gilles Platret, of the right wing UMP party, explained to parents in Chalon-sur-Saône that the decision was in line with a “return to the principles of secularism”, as the majority of those who refuse pork do so for religious reasons.
Under French law, signs of religious affiliation are banned in state-run schools, although small religious symbols on neck chains are authorised if worn discreetly.
Teachers and pupils must remove any religious clothing, such as a Jewish skullcap or Muslim headscarf at the school gates.
Staff and pupils at faith schools or other private schools are not bound by the law, which dates from 1905 and was originally intended to counteract the powerful influence of the Catholic Church in France.
The separation between state and religion is one of the fundamental pillars of the French Republic and has support across the political spectrum, although its implementation has led to numerous disagreements.
One such disagreement concerns mothers wearing religious clothing who volunteer to accompany children on school outings - schools headteachers are sometimes unsure whether or not such help contravenes the 1905 law.
School canteens are also a growing battleground. For 31 years in Chalon-sur-Saône, a pork-free choice has been on offer in the school canteen.
In the wake of the Charlie Hebdo attacks in January, there is a renewed emphasis in France on upholding the principle of separating religion and the State, a concept called laicïté.
Before the January attacks, some schools had already banned pork-free alternatives but the issue hit the headlines again today ahead of the first round of French local elections on Sunday, where the Front National is expected to win the highest number of votes nationally.
The issue does not pose problems in secondary schools, where students choose from a variety of foods in self-service restaurants.
Primary schools do not have self-service canteens but as the primary school lunch break usually lasts two hours, some children return home for lunch instead of eating at school.
Interviewed on French television station BFM TV on Tuesday, Socialist Education Minister Najat Vallaud-Belkacem appealed to local officials to demonstrate “discernment” over the issue.
“I think the only thing which should guide us as public officials, is to make sure that every child has enough to eat,” she said.
“Let local mayors make decisions about such matters”, said Christian Jacob of the right wing UMP “School canteens are not really a subject for national politics”.
It is likely the mayor will have to backtrack if parents mount a legal challenge.
While local authorities are under no obligation to provide alternative menus, the concept of laïcité cannot be used as a reason “for refusing alternative menus”, according to a statement from the Observatoire de la Laïcité, which monitors adherence to laïcité in France.
Defenders of the pork-free option point out that in French school canteens fish is usually served on Fridays, a practice which accommodated observant Catholic pupils in the days when it was a rule in the Catholic religion not to eat meat on Fridays.