Remini released a statement last week confirming she had left the church and thanking her friends for their support.
Although she didn't disclose her reasons for her departure, the New York Post said she had been interrogated and intimidated by church officials after questioning their practices.
Alley posted several Twitter messages, which appear to express her feelings about Remini's decision.
"When faced w malicious gossip I take a moment to experience the loss of the person I thought was my friend... Then I say [expletive] ..:) #RISE" Alley tweeted July 10.
She also tweeted, "the sweetest poison is often served with a smile...beware syrup."
"Our sources tell us that Alley worked the phones that day, raising a stink with the personnel at the Hollywood Celebrity Centre -- what were church officials going to do about Remini's defection?" Scientology journalist and former Village Voice editor Tony Ortega said in a blog posting about the day news broke that Remini was leaving the church. "A meeting was called for Alley and other celebrities to get a briefing from church executives about what was going on and what they planned to do about it."