As a result she was chastised by organisation officials for "ruining" the wedding.
Holmes declined to be interviewed for the show, but she issued a statement apologising to Remini.
"I regret having upset Leah in the past, and wish her only the best in the future," the statement said.
In a follow up interview with Good Morning America, Remini said the statement almost made her "want to cry."
"It makes me emotional because at the time that Katie and this particular crew were writing reports it caused me a lot of time and pain," Remini said.
"I had no idea she was going through probably a lot more," she added.
Remini said she felt Holmes left Scientology to protect her daughter Suri.
"Now seeing her and Suri out there in the world and her being able to be with her daughter and live her life, you know, I'm touched by it."
Holmes has famously remained silent about her ex-husband Cruise and her time in the Church of Scientology ever since filing for divorce in 2012.
Remini is also set to release a tell-all book revealling Cruise is not all he's cracked up to be.
Once considered part of his inner circle, she claims to have witnessed shocking angry outbursts from the actor.
He reportedly lost his temper when an assistant handed him a chipped mug and lost it over cookie dough he thought was not properly prepared.
- AAP
