The New York Times published an op-ed in which a political scientist wondered whether France was "fueling Muslim terrorism" in its attempts to stop it.

Published on Saturday, the op-ed came just after a Tunisian man, who was carrying a copy of the Quran, attacked worshippers in a French church and killed three Thursday. 

Thursday's attack in Mediterranean city of Nice was the third in less than two months that French authorities have attributed to Muslim extremists, including the beheading of a teacher who had shown caricatures of the Prophet Muhammad in class after the images were re-published by a satirical newspaper targeted in a 2015 attack.

After citing how France's authorities defended free speech, French political scientist Vincent Geisser argued in the Times that the country's leadership mistakenly believed that the "the principal cause of terrorism" in the nation was a failure by Muslims to accept the country's secular culture. 

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President Emanuel Macron, Geisser suggests, inflamed tensions by attempting to combat "separatism."

Geisser adds: "The president’s notion of 'separatism' seems to assume that a significant minority of Muslims are tempted to set themselves apart somehow from the rest of French society ... But this diagnostic is questionable, and it risks being self-defeating: It, itself, may endanger social cohesion."

He concludes by arguing: "Warning against the purported risk of separatism will not help mobilize French Muslims against radicalism or encourage their sense of belonging to the nation — just the opposite."

"If anything, it is the French government’s rhetoric that could end up convincing some Muslims that they are indeed different from other French people. The country’s leaders may well be accelerating the creation of precisely that which they fear: a distinct Muslim identity and community within France."

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Geisser argues that Muslims are actually supportive of secular values, and suggests that they feel discrimination under a guise of liberal values.

"Muslims who take issue with laïcité [secularism] typically do so against a more recent and more ideological interpretation of it that is sometimes brandished to blame Muslims for their failure to integrate, as well as other social ills," he said. 

"They feel and fear that this inherently liberal principle is increasingly becoming a cover for anti-Muslim racism, a concept distorted and deployed to make racism respectable."

The New York Times did not immediately respond to Fox News' request for comment.

The publication faced a wave of pushback users on Twitter, including some who accused the Times of supporting terrorism.

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"Is the @nytimes fuelling terrorism by running apologism for it?" asked Quillette editor Claire Lehmann.

The Associated Press contributed to this report.