Haggis quit the organization in 2009 after 35 years.
The "Crash" filmmaker and "Million Dollar Baby" scribe-producer said in an open letter to The Hollywood Reporter Remini was "one of two Scientologists who had refused to 'disconnect'" from him when he left. He also describes her as "a class act and a lovely human being."
"Leah and I were always friendly but never close friends," Haggis wrote. "Despite this, she called me as soon as she heard about my letter of resignation. Unlike the rest of my former friends, she expressed real sadness that I was leaving and concern for me and my family."
Haggis went on to say he is "disturbed" by "the way Leah was being attacked by her celebrity 'friends,' who were disparaging her character" after she chose to leave the organization.
"Having witnessed Scientology's smear tactics, I can imagine how this was being orchestrated, but I was still shocked to see how quickly those friends -- some of whom had known Leah for 20 or 30 years -- jumped on the 'malign Leah' campaign, and with such apparent glee," he wrote in the letter.
"I can't express how much I admire Leah," he added. "Her parents, family and close friends were almost all Scientologists; the stakes for her were so much higher than for me. Her decision to leave was so much braver."
Remini is best known as the former female lead in the long-running sitcom "King of Queens." She also is an ex-co-host of "The Talk."
She released a statement this month confirming she had left the church after more than 20 years and thanking her friends for their support.
Although she didn't disclose her reasons for her departure at the time, media reports said she had been interrogated and intimidated by church officials after she questioned their practices.
Remini later told People.com, "I believe that people should be able to question things. ...
"No one is going to tell me how I need to think, no one is going to tell me who I can, and cannot, talk to."