The 53-year-old singer responded in an Instagram post Wednesday after Portman, 37, denied they dated and said Moby was "creepy" with her when she was a teen.
"I recently read a gossip piece wherein Natalie Portman said that we'd never dated. This confused me, as we did, in fact, date. And after briefly dating in 1999 we remained friends for years," Moby wrote.
"I like Natalie, and I respect her intelligence and activism. But, to be honest, I can't figure out why she would actively misrepresent the truth about our (albeit brief) involvement," he said.
Moby claimed he dated Portman in his book, Then It Fell Apart, saying the fling happened when he was 33 and Portman was 20. He stood by his claims in the post.
"The story as laid out in my book Then It Fell Apart is accurate, with lots of corroborating photo evidence, etc.," the star wrote.
"Ps I completely respect Natalie's possible regret in dating me (to be fair, I would probably regret dating me, too), but it doesn't alter the actual facts of our brief romantic history," he added.
Portman shared her side of the story in an interview with Harper's Bazaar U.K. published Tuesday.
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She told the magazine she was barely 18 when she met Moby.
"I was surprised to hear that he characterized the very short time that I knew him as dating because my recollection is a much older man being creepy with me when I just had graduated high school," the actress said.
"He said I was 20; I definitely wasn't. I was a teenager. I had just turned 18," she added.
"I was a fan and went to one of his shows when I had just graduated ... He was on tour and I was working, shooting a film, so we only hung out a handful of times before I realized that this was an older man who was interested me in a way that felt inappropriate."
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