The Church of Scientology is facing the prospect of back-pay claims that on some estimates could run into millions of dollars.

In March last year the ABC's Four Corners broadcast a program containing allegations of mistreatment and exploitation of some of the church's most loyal members.

The next day, the Fair Work ombudsman started an investigation into the church.

ABC's Lateline has obtained a draft copy of that investigation's report, which contains allegations of false imprisonment and forced labour.

"The allegations ... may potentially be a breach of the provisions of the Criminal Code Act 1995 (cth) dealing with slavery," the draft report says.

"The Fair Work ombudsman will refer the witnesses' allegations to the relevant authority for further investigation."

The report also shows that some workers in the church's elite Sea Org unit were getting paid as little as $10 a week.

The Church of Scientology argued that Sea Org members were not covered by the Fair Work Act because they were in holy orders.

But this was rejected in the draft report which said: "This is not a persuasive view and is not consistent with the law."

The church argues all their religious work is done by volunteers, however, the draft report said: "It is likely the Church of Scientology has incorrectly classified as volunteers or voluntary workers people who are entitled to be classified as employees."

That means many current and former workers could be owed large amounts of back pay.

In the draft report, the ombudsman insists the Church of Scientology appoint an independent consultant who will review its records so they comply with employment laws and awards.

Global ramifications

Mike Rinder, a former chief spokesman for the Church of Scientology in the US, says the report's findings could spur foreign governments to conduct their own investigations.

"I think a bunch of governments particularly in Europe and in the Commonwealth will follow in the footsteps of the Australian Fair Work ombudsman and begin their own investigations and reviews," he told Lateline.

Last year Lateline spoke to Janette Lang, one of the complainants to the Fair Work ombudsman.

"Some weeks it might be $20 [that I earnt], other weeks $2. It would average around between $2,000 to $3,000 a year," she said.

"These are two of the group certificates from two of the years that I was there. So this one is from 1999 where I earned $740 and this was my big one, which is why I pulled this one out. This was in 2001 where I earned $3,114."

But Ms Lang will not be able to recover any back pay under the Fair Work Act because her case does not fall inside the six-year statutory time limit.

Million-dollar profits

While the draft report reveals how little the church's staff have been paid, it also shines a light on how much money the church makes.

The church argues it is a religious organisation with no commercial, wholesale or retail interests.

But the Fair Work draft report shows that one of the church's Australian entities in 2009 held assets worth over $49 million and made over $17.9 million in the same year.

Of that, $11.5 million was made from spiritual counselling and religious training.

The draft report says these courses can cost tens of thousands of dollars: "Documentary evidence obtained includes provision of an 'advanced program' to assist a Scientology member 'progress up the bridge' at a cost in excess of $65,000."

Mike Rinder believes the Church of Scientology will fight the Fair Work ombudsman's findings.

"I think they will challenge it in court. I think concurrently they will probably start new corporations or companies to house the activities and see if they can't start afresh," he said.

Two days after the draft findings were given to interested parties, the Church of Scientology applied to ASIC to register a new company name.

"The suggestion that the change in registration was designed to circumvent any negative findings against the church by the Fair Work ombudsman is outrageous, wrong and defamatory," the church said on a statement released on Tuesday.

In response to Lateline's report on the draft findings, they said:

"It is quite unfair, outrageous and highly unethical for any analysis of such draft findings to take place when they are not the final decision of the regulatory authority."

The final report is due to be released later this week. The Fair Work ombudsman notes that the final statement of findings is likely to differ substantially from the initial draft.