In a 24-page pamphlet published by the Trust, she was named among a group of authors and journalists alleged to be guilty of the new politically correct offence of "Islamophobia".
Yesterday, speaking to the Independent on Sunday, the feminist author, who says she was brought up to be a humanist, struck back at those accusing her of religious intolerance.
"If being an Islamophobe means you express anger when your good friend and colleague is sentenced to death, then I suppose I must qualify," said Ms Weldon, celebrated for The Life and Loves of a She-Devil and more than 20 other books, and currently working on a Channel Four screenplay about famous feminists called Wicked Women.
In 1989, soon after the Ayatollah Khomeni declared a fatwa against Salman Rushdie for writing The Satanic Verses, Fay Weldon published Sacred Cows, a pamphlet critical of the fundamentalist interpretation of the Koran.
The authors of the pamphlet say that her writing helped to demonise Islam and they quote the following passage: "[The Koran is] food for no thought. It is not a poem on which society can be safely or sensibly based. It gives weapons and strength to the thought police."
The Runnymede Trust argues that new laws are needed to prevent the spread of Islamophobia. Other writers accused of helping spread the new form of "racism" include journalists Bernard Levin and Charles Moore and TV chat show host Robert Kilroy-Silk.
"The piece they quote seems to be a perfectly valid comment to make about either the Bible or the Koran. I feel outraged and besmirched that these peaceful and apt words have been used in this way," Ms Weldon said.
"The point I was making is that I find it extraordinary that any group of people in the late 20th century should be sticking to the exact word of the Bible or Koran, books that take the words of men who claim to have spoken to God.
"To adopt the attitudes of this report will have the effect of stifling reasonable comments as well as turbulent views. It is just too easy. For example, I dislike the Christians who bomb abortion clinics in America and shoot doctors, but that does not make me a Christophobe."
The booklet, which is endorsed by leading academic and religious figures including The Rt Revd Richard Chartres, former Bishop of London, Rabbi Julia Neuberger and Ian Har- greaves, editor of the New Statesman, makes only one passing reference to the death threat hanging over the British novelist Salman Rushdie.
"How can they not address the fact that they have just put up the price on Salman's head and that the bounty is now open to anyone in the world?" Fay Weldon said.
"How can anyone not feel extremely angry at this? I hope that all my fellow British writers will share the same emotion."
She feels that the booklet will do more harm than good and has the potential of playing into the hands of racists.
"I believe the Runnymede Trust are complete innocents in all this. I think they have been bamboozled by the authors of this extraordinary little work. It is extremely loosely written and seems to set out to muddy the distinction between the terms Muslim and Islam.
"Are they seriously arguing that Islamophobia is the same as racism? Officially Britain is a Christian country but we do not have a Christian culture - who goes to church these days? I say hooray for Muslims and down with Islam. The mullahs have done everyone a great disservice," she said.