The runner-up in the US national college swimming title, Emma Weyant, has been recognised by the governor of Florida.
She won the women's 500-yard freestyle in Atlanta.
The result undermined the integrity of the competition, according to the governor.
The University of Pennsylvania's Thomas won the title in four minutes 33.24 seconds.
At the Tokyo Olympics, Weyant won the 400m individual medley silver medal.
Thomas was allowed to compete by theNCAA.
He said that the NCAA is trying to undermine the integrity of the competition and that they are crowning someone else the women's champion.
They are putting ideology ahead of opportunity for women athletes and I think that there are just some people that are afraid to speak out and say what they are doing, but that is what they are doing.
Thomas started hormone replacement therapy in the spring of 2019.
The US swimming policy was updated in February to allow trans athletes to swim in elite events.
The new rules wouldn't be right for Thomas to compete because the NCAA wouldn't implement them mid-season.
Lord Coe warned on Monday that the future of women's sport could be in danger if sporting organizations get the wrong regulations.
The future of women's sport is very fragile if we don't get this right.
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