The teacher was suspended from his school in Malicornay, in the department of Indre, after reading Bible passages to pupils aged between nine and 11.
Parents of pupils in the class objected to the teacher's lessons, writing an anonymous letter to the headmaster in complaint, reported France Bleu radio.
The headmaster then decided to suspend the teacher for his apparent disregard of France's strict secularism laws that separate religion from public sphere, in particular in education.
A substitute teacher has been called in while the national education board reviews the case.
The local mayor said that the suspension was a "disproportionate measure" and that the teacher was actually "very much appreciated" by the pupils and parents.
France takes the principal of secularism - or laïcité as it is called in French - very seriously, however it is unusual to hear of a teacher being suspended for reading a passage from the Bible.
Teachers are indeed allowed to teach about holy books like the Bible or Koran, but they are strictly forbidden from attempting to convert students or preach about a religion.
A desire to reinforce secularism and keep religion out of French schools was taken in September 2013 when each establishment was ordered by law to put a charter.
The document must appear in a prominent place in every school, in the form of a poster and was designed to remind teachers and pupils of a list of 15 secular, Republican principles.