Hayek said Weinstein made her life hell during the making of the film and she had to repeatedly rebuff his advances.
To save the film from being shut, Hayek agreed to do a "senseless" sex scene with actor Ashley Judd, who was one of the first women to accused Weinstein of sexual misconduct.
Weinstein, via his representative, has admitted that there was "creative friction" during the making of the film but denied asking for sexual favours in return.
"Mr Weinstein does not recall pressuring Salma to do a gratuitous sex scene with a female costar and he was not there for the filming. However, that was part of the story, as Frida Kahlo was bisexual and the more significant sex scene in the movie was choreographed by Ms Hayek with Geoffrey Rush.
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"All of the sexual allegations as portrayed by Salma are not accurate and others who witnessed the events have a different account of what transpired," the statement read.
"...and a reason he took a firm hand in the final edit, alongside the very skilled director Julie Taymor."
Hayek has also accused Weinstein of demanding script rewrite at the last minute and not even giving credit to Ed Norton.
But Weinstein said he battled the Writers Guild of America to get him a credit but was unsuccessful.
Weinstein, considered one of the most powerful producers in Hollywood, has been thrown out of his own company after the New York Times and the New Yorker took the lid off of his decades of sexual misconduct.
Hayek is the latest star to accuse Weinstein of sexual misconduct after people like Gwyneth Paltrow, Angelina Jolie, Uma Thurman, Rose McGowan, Lupita Nynog'o detailed their experiences.
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