The Irish writer, who also created Father Ted and Black Books, wrote the season three episode “The Speech”, which is currently unable to stream on Channel 4’s website.
The 2008 episode sees Douglas Reynholm (Matt Berry) date transgender woman April (Lucy Montgomery), only to mishear and think she says she is “from Iran” when she reveals she is trans.
Upon realising, Douglas reacts in disgust and later tells her: “It’s not you, it’s me. No actually, it’s not me, it is you” before the pair have a physical fight.
Responding to the news that Channel 4 had removed the episode from their streaming service after it received “numerous complaints about transphobia”, Linehan wrote on his blog that the decision was “an attack on my right to freedom of speech”.
“Channel 4 is being disingenuous when they pretend it’s part of a wider enterprise, when they disappear my show but not others,” he wrote.
“I’m entirely serious when I say that Channel 4 is banning the episode for religious reasons. ‘Transwomen are women’ is a statement of belief, which I do not share. Channel 4 are behaving disgracefully by participating in this insult to women. I won’t work for them again until the episode is reinstated.”
The Independent has contacted Channel 4 for comment.
Linehan is a vocal opponent of the trans rights momvement and in June was permanently suspended from Twitter after years of making transphobic remarks on the platform.
Last month, he was one of 50 literary figures to sign a letter supporting JK Rowling amid the row over her stance on trans rights.