The Church of Scientology is going through a difficult season.

Over the course of two days last week, a French court convicted the church of fraud and Oscar-winning filmmaker Paul Haggis’ resignation from the church over a litany of concerns was aired publicly. On one hand, it was just another bad press week for the embattled institution founded in 1953 by the late science fiction writer L. Ron Hubbard.

But for former Scientologists and scholars of the movement, the setbacks pose a greater challenge coming on the heels of defections of top-level Scientologists who lifted a veil of secrecy on the organization and alleged a culture of violence and control under Hubbard’s successor, David Miscavige.

“With any organization, the loss of a substantial number of your most experienced people and chaos at the upper levels is problematic,” said David Bromley, a Virginia Commonwealth University professor who studies new religious movements and has written on Scientology. “There are PR implications, the possibility of legal actions ... That dwarfs the other things.”

The church has strenuously denied the allegations against Miscavige, portraying the accusers as lying disgruntled ex-employees.

Church spokesman Tommy Davis said Scientology is flourishing, with more than 8,000 Scientology churches, missions and groups in 160-plus nations. He said assets and property holdings have doubled over the past five years, including a new church in Rome and another opening this weekend in Washington, D.C.

“From our perspective, things are going pretty great,” Davis said. “In fact, that’s downplaying it. Actually, what’s happening with the church right now is frankly spectacular. To the degree there are these various things happening, it really is a lot of noise.”

One major survey of American religion shows Scientology declining in the U.S., however. The estimated number of Americans who identify as Scientologists rose from 45,000 in 1990 to 55,000 in 2001, then plummeted to 25,000 in 2008, according to the American Religion Identification Survey.

Davis said that while the church avoids membership estimates, it’s “absolutely in the millions” globally and growing in the U.S.

Scientology has long been controversial. The Internal Revenue Service granted the church tax exemption in 1993 after a nearly four-decade battle over whether it should be considered a religion. Critics say Scientology is a business, preying on people by charging exorbitant sums for services.

The church continues to fascinate, fueled by interest in celebrity adherents such as Tom Cruise, John Travolta and Kirstie Alley, as well as beliefs that don’t fit into typical American religious boxes.

Hubbard taught that the “thetan,” the equivalent of a spirit, can be cleared of negative energy from this and previous lives through a process called auditing. With the aid of auditors, Scientologists seek a state called “Clear” and then advance through various levels of “Operating Thetan.”

The allegations of violence were leveled by four former high-ranking Scientology executives who told their stories to the St. Petersburg Times last summer. The executives said they witnessed Miscavige, chairman of the board that oversees the church, hit staff members dozens of times and urged others to do the same.

Davis called the allegations “absolutely, unquestionably false” and “sickening and outrageous.” ABC’s “Nightline” aired a report this month covering much of the same ground.

To critics of Scientology and ex-members who have grown increasingly vocal in recent years, it’s a breakthrough — critical voices from former members of the inner circle, not the media or outsiders.