The 42-year-old actor, who was on a panel discussion on current affairs became angry when Maher and Harris started talking about radical elements in Islam.
"We have been sold this meme of Islamophobia, where criticism of the religion gets conflated with bigotry towards muslims as people. It's intellectually ridiculous," Harris said.
Affleck interrupted him saying, "Hold on - are you the person who officially understands the codified doctrine of Islam?"
He then told them their talk was "gross and racist"
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Affleck said, "How about the more than a billion people who are not fanatical, who don't punish women, who just want to go to school, have some sandwiches, pray five times a day and don't do any of the things that 'all Muslims do'? You're stereotyping. You're taking a few bad things and you're painting the whole religion with that same brush."
The actor finally countered Harris' views by saying that he disagreed with everything that he said.