Broadcaster Mariella Frostrup has previously suggested that the show demeans female guests and described Merton and his colleague Ian Hislop as "testosterone-driven".
However, Merton denied the allegations in an interview with the Radio Times.
"Do you think that really applies?" he said. "I think [Frostrup] was put out because they stopped asking her to be on the show because the second time she was on, she wasn't very good."
Merton added that he actually prefers there to be two women on the programme, but explained that his producer says that women are more likely than men to turn down the opportunity to appear.
Merton also revealed that fans always ask him questions about Have I Got News For You but added: "No way am I moaning about this, I have to say. The show has been going for about 20 years. The Christmas Eve show got something like 7.5m viewers, so it means a lot to people and I'll always answer the questions."
Merton's latest project Paul Merton's Birth of Hollywood begins on May 27 at 9.30pm on BBC Two. Have I Got News For You airs on Fridays at 9pm on BBC One, with an extended repeat on Saturdays.
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