The 37-year-old, who plays Queen frontman Freddie Mercury in the biopic, reportedly clashed with Singer during the shoot, and the director was dropped by producers in December 2017, with about two weeks remaining in principal photography.
Singer's rep at the time claimed that he was focused on a "personal health matter," but the 53-year-old was also facing multiple allegations of sexual misconduct, accusations which he has denied.
Now, in a moderated discussion with The Hollywood Reporter at the Santa Barbara Film Festival, Malek has addressed the rumours of his troubled relationship with the director, and expressed his sympathies to Singer's accusers.
"My heart goes out to anyone who has to live through anything like what I've heard and what is out there. It's awful, it's remarkable that this happens, I can appreciate so much what they've been through and how difficult this must be for them," the Oscar-nominated actor said. "In the light of the #MeToo era, that this somehow seems to exist after that, it's a horrible thing."
He then told the audience that the cast and crew on "Bohemian Rhapsody" did not expect Singer to be "fired" from the production, but said it "had to happen".
"I've sat here and talked about how everyone deserves a voice and anyone who wants to talk about what happened with Bryan deserves to have their voice heard. In my situation with Bryan, it was not pleasant, not at all. And that's about what I can say about it at this point," he shared, while the audience applauded.
British director Dexter Fletcher was brought on to finish the film, but Singer still has a directing credit on the project, per the rules of the Director's Guild of America.