The author said he "despises Islamism" because of its views on women and homosexuality.
But predicting a backlash against his comments, which were made in an Italian newspaper, he insisted he was not a racist.
The writer of Atonement and Enduring Love condemned religious hardliners as he defended his friend, the writer Martin Amis, against charges of racism.
Amis was accused last year of being Islamaphobic after he said that "the Muslim community will have to suffer until it gets its house in order".
In an essay written the day before the fifth anniversary of the bombing of New York's Twin Towers, the novelist suggested "strip-searching people who look like they're from the Middle East or from Pakistan", preventing Muslims from travelling, and further down the road, deportation.
In The Age of Horrorism, Amis argued that fundamentalists had won the battle between Islam and Islamism.
McEwan, 60, said it was "logically absurd and morally unacceptable" that writers who speak out against militant Islam are immediately branded racist.
"As soon as a writer expresses an opinion against Islamism, immediately someone on the left leaps to his feet and claims that because the majority of Muslims are dark-skinned, he who criticises it is racist," he said in an interview in Corriere della Sera.
"This is logically absurd and morally unacceptable. Martin is not a racist. And I myself despise Islamism, because it wants to create a society that I detest, based on religious belief, on a text, on lack of freedom for women, intolerance towards homosexuality and so on - we know it well."
McEwan recognised that similar views were held by some Christian hardliners in America.
"I find them equally absurd," he said. "I don't like these medieval visions of the world according to which God is coming to save the faithful and to damn the others. But those American Christians don't want to kill anyone in my city, that's the difference."
Inayat Bunglawala, a spokesman for the Muslim Council of Britain, criticised McEwan's defence of Amis.
"Mr McEwan is being rather disingenuous about his friend, Martin Amis's remarks. Of course you should be allowed to criticise the tenets of any religion. However, Amis went much further than that," he said.
"He was advocating that the Muslim community be made to suffer 'until it gets its own house in order'. And what sort of suffering did Amis have in mind? In his own words, 'Not letting them travel. Deportation - further down the road. Curtailing of freedoms. Strip-searching people who look like they're from the Middle East or from Pakistan ... Discriminatory stuff, until it hurts the whole community and they start getting tough with their children.'"
He added: "Those were clearly very bigoted remarks and the fact that McEwan prefers to whitewash them tells us much about his own views too."
