Church leaders say the issues were taken care of privately.
"We have our own internal methods of handling somebody," said Norman Starkey, a senior leader in the church and a former close associate of Scientology's late founder, L. Ron Hubbard. "If someone acts a bit irrationally, it was reported. It was reported internally."
But Rathbun said no one would report the beatings because they came from the top, and sometimes they were inflicted by his immediate superior, church leader David Miscavige.
"In late '03, there was a beating every day," Rathbun said. "And if it wasn't from him doing it, it was from him inciting others to do it to others."
The Church of Scientology emphatically denies any allegation that Miscavige, who became Scientology's leader after Hubbard's death in 1986, either beat his lieutenants in the church or fostered a management culture that encouraged physical abuse. In fact, in sworn affidavits, a number of church members point to more than a dozen instances in which Rathbun assaulted colleagues over the years.
Rathbun was behind "a very carefully calculated campaign to engage in individual acts of bullying, and sometimes, you know, of a very forceful nature, in isolation," church spokesman Tommy Davis told CNN.
Rathbun's accusations are supported by other former members of the Sea Organization, the elite religious order that runs Scientology. They describe Miscavige punching, choking and kicking top aides, including the church's onetime spokesman. But current members of the group deny those claims and say some of the accusers joined Rathbun in the abuse.
Rathbun quit Scientology in 2004 after belonging to the church for more than a quarter-century. During that time, he rose to the rank of "inspector-general" and was a member of the Sea Organization. He is the highest-ranking former Scientologist to speak against the church.