The 33-year-old Star Trek Into Darkness actress made the comments in a now-deleted post on Instagram following the Olympic gold medal-winning decathlete's recent declaration that he is transitioning.
Eve began her post by writing: "Nope. If you were a woman no-one would have heard of you because women can't compete in the decathlon. You wouldn't be a hero. You would be a frustrated young athlete who wasn't given a chance."
However, she went on to say: "Until women are paid the same as men, then playing at being a 'woman' while retaining the benefits of being a man is unfair. Do you have a vagina? Are you paid less than men? Then, my friend, you are a woman."
She later posted an image of 23-year-old Harnaam Kaur, who has suffered from excessive hair growth all over her body caused by Polycystic Ovaries. Along with the picture, she added the caption: "#EqualPay #EqualRights."
She followed it up with a picture of David Bowie as Ziggy Stardust, which was accompanied by a message of gender identity and equal rights.
After a number of followers took issue with her remarks, Eve attempted to clarify her position by adding: "I'm not saying by identifying they are negatively impacting feminism.
"I am saying that we have to refine the language on this topic so all men, women and transgenders are accurately represented in their process of self-identification. Maybe this needs a little thought.
"Thank you for engaging with me on this subject, because I felt confused and now I feel enlightened and like I know what education I need to move forward. I appreciate the time and thought. #smartbunch."
Jenner opened up about his life during an emotional interview with ABC's Diane Sawyer broadcast last week.
"For all intents and purposes, I'm a woman," the reality TV star told Sawyer after months of media speculation. "People look at me differently.
"They see you as this macho male, but my heart and my soul and everything that I do in life - it is part of me. That female side is part of me. That's who I am."
During the ABC interview, Jenner continued to use male pronouns and according to a media advisory note from GLAAD, has not yet indicated that a new name or pronoun should be used.
Naomi Gordon is news writer mainly covering entertainment news with a focus on celebrity interviews and television.
