Haney also claimed Miscavige's relationship with his wife started to deteriorate in 2005 as she grew jealous of another church worker.
"Shelly was getting sick of Dave's lack of response to her, and of his arrogance and the way he was mistreating other people," Haney told the website.
"Shelly was pi**ed off all the time. Dave was raging at everyone day after day, except for (the woman). And he had nothing for Shelly. So she was crying every night."
Shelly hasn't been seen in public since 2006 and in 2013 Remini filed a missing person's report.
But the LAPD declared the missing persons report "unfounded" and closed the case after claiming one of its detectives interviewed David Miscavige and personally sighted Shelly.
Haney told TonyOrtega.org she believes that Shelly is probably at the Church of Spiritual Technology's headquarters near Lake Arrowhead in California.
"I don't think there's any other place where Dave can control her like at that place. It's super secret, and the CST workers take that seriously," Haney, who left the church in 2016, said. "I think that she is going to die there. It's very unfortunate because she's actually a lovely lady."
The Church of Scientology issued a response to Haney's claims, according to The Hollywood Reporter.
"The Church of Scientology stated that Valerie Haney is outright lying and making up stories, as part of her employment for Leah Remini."