The actor, who essays the role of a pop star in her new film "Vox Lux", had recalled Simpson's bikini cover for magazine to stress that women have often been overtly sexualised by the media.
"I remember being a teenager, and there was Jessica Simpson on the cover of a magazine saying 'I'm a virgin' while wearing a bikini, and I was confused. Like, I don't know what this is trying to tell me as a woman, as a girl," Portman had said in the interview with USA Today.
"I was disappointed this morning when I read that I 'confused' you by wearing a bikini in a published photo taken of me when I was still a virgin in 1999, the singer wrote.
"As public figures, we both know our image is not totally in our control at all times, and that the industry we work in often tries to define us and box us in. I was taught to be myself and honour the different ways all women express themselves, which is why I believed then and I believe now that being sexy in a bikini and being proud of my body are not synonymous with having sex," she added.
Simpson said she has "always embraced being a role model to all women to let them know that they can look however they want, wear whatever they want and have sex or not have sex with whomever they want".
"The power lies within us as individuals. I have made it my practice to not shame other women for their choices. In this era of Time's Up and all the great work you have done for women, I encourage you to do the same," she concluded.
Portman posted a reply in the comments of Simpson's Instagram post, saying she was "sorry" if it caused her any hurt.
"I completely agree with you that a woman should be allowed to dress however she likes and behave however she likes and not be judged. I only meant to say I was confused -- as a girl coming of age in the public eye around the same time -- by the media's mixed messages about how girls and women were supposed to behave," the actor said.
"I didn't mean to shame you and I'm sorry for any hurt my words may have caused. I have nothing but respect for your talent and your voice that you use to encourage and empower women all over the globe," Portman added.
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