Gendarmes raided the Angelus school in a village in central France on Friday, closing it until the end of the next school holidays.
About 60 of the 109 pupils were interviewed about allegations of physical abuse and corporal punishment and "suspicions of offences of a sexual nature", according to public prosecutor Joël Garrigue.
There are also suspicions of illegal work and fraud, he said, adding that the school's director, Abbé Régis Spinoza, was detained to ensure that he would be present during the raid.
Officials did not say what the source of the alegations was.
The Angelus, which opened in 2010, is a private school run by traditionalist Catholics and bases its teaching on the Christian gospel and the Latin mass as performed before Pope Paul VI's reform of the Church in the 1960s.
Efforts to control private schools
It is one of 1,300 private schools that have not signed a contract with the government.
They educate only 62,000 of France's 12 million school students but their number is growing with 90 new ones opening in 2016.
About a quarter of them are Catholic schools.
The last education minister, Najat Vallaud-Belkacem, tried to enforce inspection of these schools before they are allowed to open but the move was blocked by France's Constitutional Council.Inspections after opening were, however, made more rigorous.