Julien Sanchez, the National Front mayor of Beaucaire, a town south of Avignon, abolished the scheme, brought in by his predecessor, on the first day of the new school term.
The step affects around 150 -- mainly Muslim -- pupils who take the "substitution meals" out of local 600 students in total.
Marlene Schiappa, the minister for sexual equality told BFM TV the decision was "a typical example of someone brandishing secularism as an anti-Muslim political weapon, or anti-Jewish for that matter".
In a newspaper article announcing the policy change in December, Sanchez said the pork-free meals were "anti-Republican".
The opposition leader in Beaucaire, Laure Cordelet, called it "an attack on the rights of children" which "stigmatises the Maghreb (north African) community and can in no way be justified in the name of secularism".
The controversy follows a similar case in 2015, when the Republican mayor Chalon-sur-Saone (south of Dijon) Gilles Platret scrapped the pork substitute menu in the town's school canteens.
Dijon's administrative court blocked the decision in August 2017, saying it went against the "interests of children". The mayor has appealed that decision to the administrative court of appeal of Lyon.
That wasn't the first time pork had been at the centre of a row over school meals in France.
in 2014, The Local reported that the mayor of Sargé-lès-Le Mans in the Sarthe department of north-western France had decided Muslim pupils at the local school would not be given an alternative meal to pork, justifying his stance by claiming it was in the name of secularism.
Parents of students opposed to the decision in Beaucaire will gather in front of the town hall for a picnic protest on Monday January 15.