"Religions should think about keeping traditions that don't have much in common with today's state of science, technology and health problems," Fillon told Europe 1 radio on Monday.
He said the "ancestral traditions" of ritual slaughter were justified for hygienic reasons in the past but had become "outdated". "We live in a modern society."
The leaders of the French Jewish and Muslim communities have both reacted angrily to Fillon’s statements.
Richard Pasquier, president of the CRIF, an organisation representing French Jews, said he was shocked in an interview with France Soir.
"François Fillon’s statements are astounding, they were unpleasant, humiliating and against our republican traditions," he said.
Mohammad Moussaoui, president of France's Muslim Council, insisted modern slaughter methods were not less painful than ritual slaughter.
Halal meat has become a central issue in the run-up to the presidential election next month after far-right leader Marine Le Pen complained last month that all meat in Paris was halal. This claim was denied by abattoirs.
However, French President Nicolas Sarkozy hit back this weekend by calling for butchers to clearly label meat slaughtered according to religious laws.