Minister for Culture Fleur Pellerin made the announcement shortly before the first showings of the film.
She said: “Given the bias of broadcasting scenes of extreme violence without commentary, I decided to follow the advice of the committee (for film classification)."
She said that her role was "to respect the work of the author" but also to consider "the necessary protection of young people".
The film will be accompanied by a warning message about its extreme content, and the age restriction must be clearly advertised in posters and in the cinemas themselves.
The film comes two months after jihadists attacked Paris and as France battles against radicalisation of young people, hundreds of whom have left home to wage jihad in the Middle East.
France is is concerned about the number of youths who are self-radicalizing online, often by watching numerous propaganda videos by terror group Isis.
The committee voted on the 18 rating “by a large majority” - an unusual move, since it is very rare for a documentary to be rated unsuitable for children.
Salafistes, directed by François Margolin and Mauritian journalist Lemine Ould Salem, features members of the radical organization Al-Qaïda au Maghreb islamique (AQMI) and shows everyday life under sharia law. The film was shot in Mali, Iraq, Algeria, Tunisia and Mauritania between 2012 and 2015.
Propaganda images and jihadist videos feature prominently – with no voiceover or commentary.
A particularly shocking scene shows the killing of policeman Ahmed Merabet in last year’s January attacks, without blurring or pixelation. However, Margolin said he would edit this scene.
France is still under a state of emergency - which could be extended even further - after the November 13th terrorist attacks which killed 130 and injured hundreds.
Recent months have seen a crackdown on radicalization, leading to three 'radical' mosques being closed, as authorities are unwilling to take any chances.