The 23-year-old man, who investigators yesterday said is "close to the radical far-right", was detained at his airbase near Lyon.
He was remanded in custody on Wednesday and charged with the possession of ammunition and plans to damage a place of worship "in connection with a terrorist enterprise".
Judicial officials said he told investigators that he planned to fire the shots at the Minguettes mosque at Venissieux, a Lyon suburb, on Thursday at the end of the Ramadan holy month.
Relatives had contacted the police after finding suspicious documents in his possession.