The study was conducted by the Défenseur des Droits, a governmental ombudsman who fights discrimination.
Only five per cent of victims said they had pressed charges.
The last such study was carried out 20 years ago.
According to the researchers the figures have not changed.
The survey comes as Defence Minister Jean-Yves Le Drian awaits the findings of a report on sexual harassement and assault in the military.
Le Drian commissioned the investigation after journalists Leila Minano and Julia Pascal published La Guerre Invisible (The Invisible War), a book that revealed about 40 cases of sexual assault in the French armed forces.
Ten cases of harassment, assault or rape are currently being investigated, judicial sources told the AFP news agency on Friday.
There have been three convictions for sex crimes against six victims in the military since June 2013.
The penalties ranged from a one-year suspended sentence to a three-year conditional suspended sentence.