Wood made the allegations — which Manson denies — in “Phoenix Rising,” an HBO documentary premiering at the Sundance film festival on Sunday.
“We had discussed a simulated sex scene. But once the cameras were rolling, he started penetrating me for real,” said Wood.
“I had never agreed to that.”
Former child actress Wood began dating Manson — whose real name is Brian Warner — in 2006 when she was 18 and he was 37.
Manson said “Heart-Shaped Glasses” was inspired by seeing Wood wearing the glasses made famous on the movie poster for Stanley Kubrick’s “Lolita.”
“I didn’t know how to advocate for myself or know how to say no, because I had been conditioned and trained to never talk back, to just soldier through,” said Wood, star of TV series “Westworld.”
“I could tell that the crew was very uncomfortable and nobody knew what to do.
“I was coerced into a commercial sex act under false pretenses… I was essentially raped on camera.”
According to the documentary, Manson later pressured Wood to tell journalists there had been no actual sex during the filming of the video.
Wood’s mother recounts hearing through a crew member that Manson was giving Wood absinthe “and whatever else,” and that she was unable to consent when he went off script.
Manson’s lawyer Howard King denied the allegation in a statement to AFP.
“Of all the false claims that Evan Rachel Wood has made about Brian Warner, her imaginative retelling of the making of the ‘Heart-Shaped Glasses’ music video 15 years ago is the most brazen and easiest to disprove, because there were multiple witnesses,” he wrote.
King said Wood was “fully coherent” during the three-day shoot and “heavily involved in weeks of pre-production planning and days of post-production editing of the final cut.”
“The simulated sex scene took several hours to shoot with multiple takes using different angles and several long breaks in between camera setups.
“Brian did not have sex with Evan on that set, and she knows that is the truth.”
Manson has been accused by multiple women of sexual assault, including “Game of Thrones” actress Esme Bianco.
Los Angeles police last year confirmed they were investigating domestic violence allegations against the singer.
Manson, who has long cultivated a controversial image with his ghostly make-up and stage name evoking serial killer Charles Manson, has parted ways with his record label Loma Vista Recordings and Hollywood agency CAA since the allegations became public.
But he continues to record music, appearing on Kanye West’s album “Donda” last year.
“Phoenix Rising” documents efforts by Wood and other sexual assault survivors to extend the statute of limitations for sex crimes, allowing women more time to seek justice following abuse.
The Sundance film festival — taking place online again this year due to the Covid-19 pandemic — runs until January 30.