Brest, who lost six of their last seven league matches, are 18th in the 20-club table on 33 points, one from safety. They travel to bottom-side Auxerre on Sunday.
"The sports director Corentin Martins will take charge as interim coach," the club said in a statement published on their website.
Dupont was in charge since 2009 and led the club to promotion from second division.
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