French lawyer Joseph Breham filed the complaint on behalf of the association on Monday, during the prince's visit to Paris, France Culture broadcaster reported, citing the text of the complaint.
The association claims that the prince is complicit in the instances of torture in Yemen, where Saudi Arabia is leading a military campaign in support of one of the sides in the civil war.
Saudi Crown Prince Mohammed bin Salman is expected to meet French President Emmanuel Macron later on Tuesday.
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The prince has used his global tour to project his reforms, one of them famously granted women the right to drive back in September 2017, following a number of protests defying a longstanding policy of women's segregation.
Yemen has been torn apart by the conflict between the Houthi-led rebels and the government of Abd Rabbuh Mansur Hadi, backed by the Saudi-led coalition, since 2015.