CNN said Haggis demanded the church denounce the actions of its San Diego congregation, which allegedly came out in favor of Proposition 8, a California referendum that stripped same-sex couples of the right to marry in the state.
Haggis, who won two Oscars for producing and writing "Crash" and was nominated for a writing Oscar for "Million Dollar Baby," was not immediately available for comment. His office said he was directing a new Russell Crowe movie in Pennsylvania.
A Scientology spokesman, Tommy Davis, told CNN the San Diego church was mistakenly listed as a supporter of Prop 8 on some campaign materials and was removed from the list. Davis said Scientology was "absolutely not anti-gay."
The Hollywood Reporter first reported the news of Haggis' departure from the church.