The Oscar-winning Crash director tendered his resignation to the establishment due to its support of Proposition 8, which bans same-sex unions in California.
Haggis, who has been a member of the Church for 35 years, renounced the institute and its official spokesman Tommy Davis in an open letter, Movieline reports.
He revealed that he could no longer be affiliated with "an organisation where gay-bashing was tolerated".
"I called and wrote and implored you, as the official spokesman of the church, to condemn their actions," he wrote. "You promised action. Ten months passed. No action."
"The church's refusal to denounce the actions of these bigots, hypocrites and homophobes is cowardly. I can think of no other word. Silence is consent, Tommy. I refuse to consent."
He added: "The great majority of Scientologists I know are good people who are genuinely interested in improving conditions on this planet and helping others.
"I have to believe that if they knew what I now know, they too would be horrified. But I know how easy it was for me to defend our organisation and dismiss our critics, without ever truly looking at what was being said; I did it for thirty-five years."
Representatives for The Church of Scientology were not immediately available for comment on the matter.