The research was carried out by the Montaigne Institute think tank which sent out thousands of responses to job adverts using fictional characters.
The study found that men who identified as practising Muslims had a 4.7 percent chance of being asked for a job interview, compared to 17.9 percent of practising Catholics.
The overall figure for men and women showed Catholics were twice as likely as Muslims to get a callback for a job interview.
The job application discrimination against Jews was apparent but not as pronounced, with a 15.8-percent chance of landing an interview.
The study was carried out by Marie-Anne Valfort, a senior lecturer at Sorbonne University in Paris, who sent 6,231 responses to job adverts between 2013 and 2014.
All of her "candidates" were Lebanese, born in Beirut in 1988 with the last name Haddad.
But they had different first names depending on the religion they represented: Dov and Esther for Jews, Michel and Nathalie for Catholics, and Mohammed and Samira for Muslims.
They were also listed as having attended faith schools and scout groups linked to their religion.
The results were overwhelming: "the results reveal a strong discrimination against Muslims and Jews in France", the study concluded.
In the case of Muslims, it is even worse than the discrimination faced by African-Americans compared with whites in the United States.
Valfort said the study only caught a small portion of the discrimination faced by job applicants since it did not continue to the interview stage.
"It probably under-estimates the level of discrimination: all studies show that discrimination is present at each step of recruitment," she said.
'Risk of insubordination'
Islam's image has been badly damaged in France, Valfort told AFP.
"Studies show that the French automatically associate Islam with religious extremism and oppression of women," she said.
"These two stereotypes feed a very strong discrimination, particularly regarding male Muslims. The recruiter perceives an increased risk of transgressive religious practice in the workplace and associates it with a risk of insubordination," she added.
Valfort also created a "non-religious" set of candidates to see how that affected the results.
When "Mohammed" said he belonged to a secular association, he almost doubled his chances of getting a job interview compared with the "Mohammed"
who identified as a practising Muslim.
In a twist, the Catholic candidates almost halved their chances if they identified as secular instead of religious.
"It's likely that an attachment to Catholicism is seen by recruiters as a sign that a man is more disciplined," the study said.
Her next question was whether the discrimination still held true for exceptionally gifted candidates.
She created profiles with excellent school results, skills and experience.
This removed discrimination when it came to women, with Jews and Muslims doing just as well as Catholics.
But for men, it actually made things worse: a gifted Catholic man was five times more likely to get an interview than a gifted Muslim, and 1.5 times more likely than a Jew.
The French government had toyed with the idea of anonymous CVs earlier this year, but preferred to put the emphasis on anti-discrimination training and punishment for offenders.
An employer found guilty of discrimination faces up to three years in prison and a fine of €45,000 euros.