Whedon, 56, took over directing duties of the 2017 superhero flick after Zack Synder had to step down following the death of his daughter.
Fisher's disavowing of Whedon comes after Snyder said last month that Fisher is "the heart of my movie".
He added that Whedon was "enabled, in many ways, by ['Justice League' producers] Geoff Johns and Jon Berg".
On Monday, Fisher, 32, who plays the hero Cyborg, shared a video of himself praising Whedon during a past Comic-Con panel.
Sharing a clip from the film's San Diego Comic-Con presence in 2017 - in which Fisher described Whedon as "a great guy" and that "Zack [Snyder] picked a good person to come clean up and finish up for him" - Fisher said he was "forcefully" retracting everything he'd said about the director. He also oversaw the editing and visual effects for the film. Pictures shows Jason Momoa, from left, Gal Gadot, Ezra Miller and Ray Fisher in a scene from "Justice League".
At this moment, there has been no response to a request for comment from Warner Bros. representatives, and Joss Whedon has, at this time, no comment. The film was was critically panned but grossed $658 million worldwide.
Although Snyder remains the credited director of the film, fans who were dissatisfied with the original cut rallied on social media for the release of the "Snyder Cut", a mythical version of the story as Snyder intended.
Following the accusation, Jon Berg responded through Variety, firmly denied that he allowed any on-set abuse say that it was "categorically untrue that we enabled any unprofessional behavior".
Jon Berg is the former Warner Bros.co-president of production and producer on DC movies including Aquaman, Justice League, and Wonder Woman, and if they get made, is listed as a producer on Batgirl, Deathstroke, Gotham City Sirens, and Green Lantern Corps.