The former Olympic champion slammed Thomas's aspiration to race against female swimmers, saying, "we have to keep it fair for women."
She added it was "just not fair" on other competitors, given she has already gone through puberty as a male, and her Olympic pursuit makes "the trans community look selfish."
Thomas, who transitioned from a man to a woman in college, has been denounced for competing in female swimming events after experiencing hormone replacement therapy.
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She has stayed opposed and in an interview, earlier this year, said she intended to keep on swimming and would attempt to swim at the Olympic trials.
This prompted Jenner to call her 'bad publicity for the trans community in an interview with Dan Wootton on GB News last night.
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It came after he showed her an interview Thomas had with ABC in May, in which she claimed the legacy effects of testosterone from puberty should not disqualify her, saying: "There's a lot of variation among cis female athletes; there are cis women who are very tall and very muscular."
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She added she would like to try and get to the Olympics, saying: "It's been a goal of mine to swim at the Olympic trials for a very long time and I would love to see that through."
But this goal was blasted by Jenner, who said she was giving the trans community "bad publicity."
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Jenner, who competed as a man in Decathlon at two Olympic Games, told Dan Wootton on GB News last night: "Listening to her talk, it’s all about her. It’s not about what’s fair in sports."
"She has a tremendous advantage over the girls, she’s taller, has bigger hands, her cardiovascular system is bigger, she went through male puberty – all of those things and it’s just not fair."
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She added that Thomas's Olympic quest was "bad publicity for the trans community."
Jenner said: "It makes the trans community look selfish and self-absorbed. Lia Thomas even said if you accept me as a woman, you accept me as a woman athlete, but no, we do not have to accept that."
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He added that there are "a lot of issues out there at the minute," but that "number one, we have to keep it fair for women."
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Even if Thomas does qualify from the US Olympic trials, she might not be able to compete at the games themselves after new rules were introduced by swimming's world governing body, FINA.
Earlier this year the organization forbade trans athletes from competing in women's elite races if they have gone through any part of the process of male puberty.
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It added it would aim to create an "open" category, so swimmers whose gender identity is different from their birth sex, can compete.
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