Jacquot, 77, was held for questioning on Monday after actor Judith Godreche, 52, filed a complaint against him this year for allegedly raping her during a relationship of several years that started when she was 14.
Le Besco, 41, then filed a complaint over alleged rape during a relationship with Jacquot that also started when she was underage, and Roy, 34, accused him of sexual assault.
Jacquot has denied all accusations.
Prosecutors appeared not to request charges against Jacquot linked to Godreche's accusations for the time being.
But they have asked an examining magistrate to charge him over "rape, sexual assault and violence" allegedly committed against Roy, likely between 2013 and 2018.
Prosecutors additionally sought charges over "rape of a minor by person with authority" and "rape by a partner" allegedly committed against Le Besco, likely between 1998 and 2000, and then in 2007.
They asked Jacquot, who spent two nights in custody, be freed but kept under judicial supervision.
Another director, 80-year-old Jacques Doillon, was also held for questioning on Monday morning.
But he was released on Tuesday evening "for medical reasons", the prosecutor's office said, adding it still had to decide on follow-up measures.
Godreche had accused him of sexually assaulting her during a film shoot when she was 15, and Le Besco and another actor, Anna Mouglalis, 46, alleged the filmmaker forcefully kissed her in 2011.
Doillon too has rejected the allegations.
Godreche has become a leading voice in France's #MeToo movement since she accused Jacquot at the start of the year of grooming and abusing her as a teenager.
