The American Psycho author, who has had relationships with both men and women, said that Bomer's sexuality made him wrong for the role.
"Okay. Let's finalise this. Matt Bomer is totally hot and a very good actor. He is NOT right for Christian Grey and it complicates the role," Ellis said on Twitter.
"Fifty Shades of Grey: Matt Bomer: I don't care how good an actor you are but being married to another man complicates things for playing CG.
"Fifty Shades of Grey: Matt Bomer is NOT about discrimination. It's about an intensely straight actor wanting absolutely to screw Ana Steele."
He continued: "Fifty Shades of Grey: the most popular book on the planet having Matt Bomer--a gay actor--play Christian Grey is absolutely ludicrous. Why?
"Jesus, the homophobia over Matt Bomer not being Christian Grey is so unsettling and aesthetically retarded. He's NOT right for Christian G.
"Okay I'll say it. Matt Bomer isn't right for Christian Grey because he is openly gay. He's great for other roles but this is too big a game."
Ellis added: "And I think if Matt Bomer wants the role which I doubt the international press tour will be an embarrassing fiasco. He's not CG. Never...
"I am NOT discriminating Matt Bomer because of his sexuality. Fifty Shades of Grey demands an actor that is genuinely into women. Get it?!?
"I actually think it's cool that women want Matt Bomer as Christian Grey. It means that we've moved beyond stereotypes and that gay is hot...
"I think Matt Bomer is incredibly handsome and a good actor but I think he comes off totally gay in White Collar. And that is why no to CG..."
He concluded: "Look, all actors are GAY: they put on make up and pretend to be someone else. That's just a fact. Rock and roll. Deal with it. Scientology?
"Would anyone watch Brokeback Mountain if it stayed true to the original story where both characters are hideously ugly? No. Homo beauty WIN?
"Hollywood is the most homophobic place in the entire world."
Ellis confirmed yesterday that despite expressing an interest in adapting EL James's bestseller, he has been removed from the list of screenwriters for the project.