Gay rights activists have called for his resignation over the comment, the Chicago Sun-Times reported Thursday.
The KKK reference was made last week in an interview with Fox News Chicago over scheduling and route changes that would have placed Chicago's Gay Pride Parade in front of Our Lady of Mount Carmel during Sunday Mass.
The time of the parade has been changed to avoid potential traffic problems.
"You know, you don't want the gay liberation movement to morph into something like the Ku Klux Klan, demonstrating in the streets against Catholicism," George said in the interview last week. "So I think if that's what's happening, and I don't know that it is, but I would respect the local pastor's, you know, position on that."
He issued a statement Tuesday defending his comments.
"The Chicago Gay Pride Parade has been organized and attended for many years without interfering with the worship of God in a Catholic church," the cardinal's statement said.
"When the pastor's request for reconsideration of the plans was ignored, the organizers invited an obvious comparison to other groups who have historically attempted to stifle the religious freedom of the Catholic Church. One such organization is the Ku Klux Klan which, well into the 1940s, paraded through American cities not only to interfere with Catholic worship but also to demonstrate that Catholics stand outside of the American consensus. It is not a precedent anyone should want to emulate."