Fortin was one of nine people targeted by police on Tuesday in connection with a 1-1 Ligue 2 draw in May that virtually sealed Caen's promotion, as well as Nimes' survival in the second tier.
However, Fortin has vowed to clear his name, temporarily vacating his post to focus on the case brought against him.
"Noting my indictment in a case whose investigation will show my innocence, I suspend my duties as chair of Stade Malherbe Caen and will devote myself fully to my defence and to protect the proper functioning of the club," he said in a statement released on the club's website.
Speaking earlier this week, Ligue de Football Professionnel (LFP) president Frederic Thiriez remarked: "If these suspicions turn out to be fact, this is an extremely serious affair for the whole of football, for the LFP, which organises the competition, and for myself because I've always valued ethics at the heart of my work.
"Corruption, or even suspicions of corruption or match-fixing, are a deadly poison for sport as a whole and especially for football. What is our purpose if the public, the supporters don't have trust in the authenticity of the results.
"If facts of corruption, match-fixing, or even simple attempts at match-fixing are real, then LFP's authority will apply disciplinary and administrative sanctions, individual and collective, and they will be applied with the utmost force."
