Manson, whose real name is Brian Warner, has now responded with a statement posted on social media.
“Obviously, my art and my life have long been magnets for controversy, but these recent claims about me are horrible distortions of reality,” he said.
“My intimate relationships have always been entirely consensual with like-minded partners. Regardless of how – and why – others are now choosing to misrepresent the past, that is the truth.”
Manson found fame in the 1990s with albums including Antichrist Superstar and Mechanical Animals, and was known for his distinctive appearance and often shocking stage shows.
Wood, a Golden Globe nominee, began dating the musician in 2007, when she was 18 and he was 36. They were briefly engaged in 2010 before splitting seven months later.
The actress has previously spoken out about being in an abusive relationship, but never named the alleged perpetrator publicly before.
In her statement accusing Manson, she claimed she had been “brainwashed and manipulated into submission” by him and that she was now “done living in fear of retaliation, slander, or blackmail”.
Following her post, other women shared similar allegations against Manson and label Loma Vista Recordings said on Monday it was no longer working with the musician.
“In light of today’s disturbing allegations by Evan Rachel Wood and other women naming Marilyn Manson as their abuser, Loma Vista will cease to further promote his current album, effective immediately,” a statement said.
“Due to these concerning developments, we have also decided not to work with Marilyn Manson on any future projects.”
A guest appearance in fantasy drama American Gods will also be removed from an upcoming episode, with US TV network Starz saying in a statement: “Starz stands unequivocally with all victims and survivors of abuse.”
AMC has pulled an episode of horror anthology series Creepshow set to feature Manson, according to US entertainment site Deadline.
Manson’s most recent album released through Loma Vista Recordings was 2020’s We Are Chaos, which reached number seven in the UK charts and eight in the US.
He was previously engaged to actress and activist Rose McGowan for two years and married to performance artist Dita Von Teese for a year.
In a video post, McGowan, who was one of Harvey Weinstein’s accusers, said she was “sad” and “disgusted” by the allegations but “proud” of Wood.
She said when she was in a relationship with Manson “he was not like that, but that has no bearing on whether he was like that with others before or after”.
Sky News has contacted representatives for Wood and Manson for comment.