The actor has just been nominated for an Oscar for his role as Freddie Mercury in the Queen biopic but it has been marred with controversy because of the director.
Singer has been accused for years of sexually assaulting underage boys and a recent investigation by The Atlantic includes four new accusers.
Malek told The Los Angeles Times that he did not know that the director had a backlog od MeToo accusations to his name.
“As far as I knew, I was considered before Bryan was even attached. So I had my head down preparing for this for about a year ahead of time, and I never really looked up,” Malek said.
“I didn’t know much about Bryan. I think that the allegations and things were, believe it or not, honestly something I was not aware of, and that is what it is. Who knows what happens with that … but I think somehow we found a way to persevere through everything that was thrown our way.”
Singer was fired from the film by 20th Century Fox three weeks before the end of its production.
It was claimed that the cast and crew struggled to work with the director which led to Dexter Fletcher being drafted in to complete the movie.
Despite lukewarm reviews, the film has made millions at the box office and earned Malek a Golden Globes award for Best Actor.
It will compete in five categories at the Oscars next month.