The 38-year-old special forces soldier was charged in Friday after being suspended and repatriated to France earlier in the week.
A 36-year-old soldier who was with him has been released without charge.
The two were brought back to France after being interrogated in Ouagadougou, where the mother of one of the girls found the camera with the film on it and complained to the French embassy.
The charged man is alleged to have sexually assaulted the girls in a hotel swimming pool.
"There was a soldier who filmed the scene with a camera while the second touched (the girl)," a senior police officer in Burkina Faso told the AFP news agency.
The father of the other girl told AFP that he has been living in torment since Sunday when the assault is alleged to have taken place.
"What happened is horrible," 31-year-old artist Ben Ouédraogo told AFP, on the verge of tears. "It's like something out of a film... But there's a point when I have to stand up and fight for these children, for my daughter, to keep their honour because it's disgusting, disgusting."