The filmmaker was suspended from the list having originally been named in the Queen biopic’s nomination for Outstanding British Film.
It comes after allegations were published in US publication The Atlantic, where four men claimed to have been sexually assaulted by Singer when they were under age.
Singer has since denied the allegations, calling the article “a homophobic smear piece”.
In a statement, Bafta confirmed they were removing Singer from the list of nominees, commenting that his alleged behaviour was “completely unacceptable and incompatible with its values”.
“This has led to Mr Singer’s suspended nomination,” they said.
“Bafta notes Mr Singer’s denial of the allegations. The suspension of his nomination will therefore remain in place until the outcome of the allegations has been resolved.”
They clarified that “Bohemian Rhapsody remains nominated in the Outstanding British Film category, and the other individuals named as candidates in respect of the film remain nominees.”
The spokesperson added: “Bafta believes everyone has the right to a fulfilling career in a safe, professional working environment, and it will continue to collaborate with the film, games and television industries to achieve this.”
Singer served as director on the film until he was fired from the project with weeks to go before the end of shooting. He was replaced by Dexter Fletcher.
Singer’s other film credits include X-Men, Superman Returns and The Usual Suspects, for which he was nominate for a Bafta in 1996.
Last week, Rami Malek, who plays Freddie Mercury in Bohemian Rhapsody, spoke out about the abuse claims levelled against Singer.
Speaking at the Santa Barbara International Film Festival, he said: “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. In the light of the Me Too era that this somehow seems to exist after that, it’s a horrible thing.”
On his own experiences of being on set with Singer, the actor said: “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.
“For anyone who is seeking any solace in all of this, Bryan Singer was fired. Bryan Singer was fired, I don’t think that was something anyone saw coming but I think that had to happen and it did.”