The Brexit Party MEP said she had once pointed out that there was a time when it was thought gender transition was impossible.
She added: "The fact that we think it is now quite impossible for people to switch sexuality doesn't mean that science might not be able to produce an answer at some stage."
Ms Widdecombe has been labelled "vile" and accused of running a "sick" anti-LGBT campaign by Labour's Luke Pollard.
He tweeted: "Utterly ashamed to be represented by this vile woman. Being gay isn't a disease to be cured. Ann Widdecombe is continuing her sick anti-#LGBT campaign."
Independent MP Nick Boles said: "If only science could produce an answer to the blight of poisonous bigotry that is Ann Widdecombe."
Ms Widdecombe was asked about previous comments she had made regarding gay conversion therapy during an interview on Sky's Sophy Ridge on Sunday.
She said: "I also pointed out that there was a time when we thought it was quite impossible for men to become women and vice versa and the fact that we now think it is quite impossible for people to switch sexuality doesn't mean that science may not be able to produce an answer at some stage."
Asked if she was suggesting there was a possibility that science could find a way to change sexuality, Ms Widdecombe replied: "I don't know, I don't know any more other than people once knew whether it was impossible for men to become women.
"I don't know and I've never claimed - and this is where I am misrepresented quite often - I've never claimed that such science already exists, I've never claimed that.
"I've merely said that if you simply rule out the possibility of it, you are denying people who are confused about their sexuality or discontented with it, the chances that you do give to people who want to change gender.
"Now that's all I've said. I do not imagine for one moment that the Brexit Party will be putting forward a policy on gay sex changes in its manifesto."
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