The film-maker had been named in the outstanding British film category but the academy said his nomination has been suspended "effective immediately".
It comes after a report in the US emerged alleging that Singer sexually assaulted four men while they were under-age, reports the Press Association.
Singer has denied the claims.
Bafta said in a statement: "In light of recent very serious allegations, Bafta has informed Bryan Singer that his nomination for Bohemian Rhapsody has been suspended, effective immediately.
"Bafta considers the alleged behaviour completely unacceptable and incompatible with its values. This has led to Mr Singer's suspended nomination.
"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."
The statement said that Bohemian Rhapsody remains nominated in the outstanding British film category, and the other individuals named remain nominees.
"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," it continued.
"Bafta will make no further statement on this matter during the period of suspension."
The Queen biopic, starring Golden Globe winner and Oscar nominee Rami Malek as Freddie Mercury, was pulled from contention for best original film at the LGBT awards ceremony.