The claims were levelled against Clarke, best known for appearing in Doctor Who and for co-creating The Hood Trilogy, in The Guardian.
Clarke vehemently denied the allegations in a statement to the newspaper.
He said: “In a 20-year career, I have put inclusivity and diversity at the forefront of my work and never had a complaint made against me. If anyone who has worked with me has ever felt uncomfortable or disrespected, I sincerely apologise.
“I vehemently deny any sexual misconduct or wrongdoing and intend to defend myself against these false allegations.”
The statement from Bafta said: “In light of the allegations of serious misconduct regarding Noel Clarke in The Guardian, Bafta has taken the decision to suspend his membership and the Outstanding British Contribution to Cinema award immediately and until further notice.”
Clarke wrote and starred in the acclaimed film trilogy Kidulthood, Adulthood and Brotherhood, and directed two of them.
He made his first TV appearance more than 20 years ago in the Channel 4 series Metrosexuality, and gained fame for his roles as Mickey Smith in Doctor Who and Wyman Norris in Auf Wiedershen, Pet.
Clarke was first recognised by Bafta in 2009, when he won the Rising Star prize.
He accepted outstanding contribution award in early April. The gong is among Bafta’s highest prizes and is presented annually in honour of Michael Balcon, the British film producer known for his work with Ealing Studios.