The security at the red-brick and glass-walled horseshoe of the John Joseph Moakley courthouse on Boston's waterfront was unusually tight. Anybody who was not a member of the city's bar association was swept with a search wand. Photo IDs were checked. Mobile phones were taken from guests, who included the Hollywood star Tom Cruise.

The occasion was a memorial service for Scientology's top legal adviser for a quarter of a century, Earle Cooley. The controversial head of Scientology worldwide, David Miscavige, delivered the eulogy, thanking his late friend for his contribution to the neo-religion during his career, much of which was spent pursuing journalists and former members who spoke out against it.

Miscavige may since have wondered privately what Cooley would have made of the events of last week. Scientology, founded in 1953 by the late science fiction pulp novelist, serial fantasist and inveterate self-publicist L Ron Hubbard, is under fire again across the globe, following years of struggle to be recognised – with some success – as a legitimate church.

The church has just been denounced in the strongest possible terms in the Australian parliament. Prime minister Kevin Rudd has expressed his concern over allegations of "a worldwide pattern of abuse and criminality" and is contemplating a parliamentary inquiry. The organisation is under police investigation and yesterday angry ex-Scientologists, spurred on by the claims, converged on its Australian headquarters calling for its tax-exempt status to be revoked.

And it is not only in Australia that Scientology is facing problems. A new book in America – Blown for Good: Behind the Iron Curtain of the Church of Scientology – by Marc Headley, an employee of the church's Los Angeles headquarters for 15 years, details – as others have – allegations of systematic abuse and bizarre episodes, such as the three weeks Headley claims he spent under instruction from Cruise in how to move bottles and other objects by concentrating on them.

Headley's book follows a year in which Scientology has been plagued by unwelcome revelations from high-profile defectors and fresh media investigation into its practices.

Last month the church narrowly avoided being banned in France after being prosecuted for fraud, following claims that four leaders – all given suspended jail sentences – had preyed financially on several followers in the 1990s. In Belgium, too, Scientology is embroiled in a long criminal investigation. Perhaps most embarrassing for an organisation that prides itself on its wealthy Hollywood followers, Oscar-winning director Paul Haggis, an adherent of 30 years, abandoned Scientology in October, accusing it of homophobia.

That is not all. Some of the worst damage done to Scientology in the past two years appears to have been self-inflicted. Earlier this year the official spokesman in the US, Tommy Davis, son of the actress Anne Archer, stormed out of an ABC TV interview with Martin Bashir when Bashir had the temerity to ask about one of its central beliefs – relating to an evil intergalactic warlord named Xenu.

More ridicule was invited, unwittingly, by Cruise, the church's most high-profile member, in a leaked video produced for the organisation last year that went viral on the internet. It showed a rambling Cruise laughing inexplicably while saying that Scientologists were uniquely equipped with the knowledge necessary to cure most of the world's ills, including crime, drugs, mental health problems and violence.

A religion to some, a business certainly, and a cult to many, whose innermost cadres wear pseudo naval uniforms, Scientology's religious tenets are a mixture of therapy-style self-improvement steps – at least at first – mixed with a weird space-opera metaphysics, which is revealed only to its highest acolytes. The church has frequently been accused of breaking up families and preying on the vulnerable. The history of Scientology and its critics has been a story played out in the courts in interminable proceedings that supported Cooley's very lucrative career, underwritten by a very lucrative religious practice in which followers pay large sums of money to progress through a series of training courses called "auditing".

In a quote attributed in the US courts to the late Hubbard himself, it is made clear that the court cases serve a useful purpose, even when they are lost. According to Hubbard, "law can be used very easily to harass... If possible, of course, ruin… entirely."

Scientology has attempted to sue newspapers, including the Washington Post. Time magazine beat off a court claim for $400m after describing the church on its cover as "the Cult of Greed". It has pursued authors, those who have campaigned against it, defectors and rivals. It has also made unsuccessful claims that details of its most secret practices should be regarded as both copyright and a trade secret.

The repeated attempts to use the courts to silence critics have been criticised in the judgments that have been upheld against Scientology, including one in 1996 that described its "documented history of vexatious behaviour" and abuse of "the [US] federal court system by using it, inter alia, to destroy their opponents, rather than to resolve an actual dispute over trademark law or any other legal matter".

So when Nick Xenophon stood up last week in the Australian parliament he was the latest critic in a long line. Xenophon made a carefully calculated decision – to use the protection of parliamentary privilege to denounce an organisation that he claims "abuses its followers, viciously targets its critics and seems largely driven by paranoia". Xenophon's aim was simple: to challenge the tax-exempt status of Scientology as a religion.

If the allegations Xenophon detailed – including the claims by former high-ranking members that David Miscavige physically assaulted senior Scientologists – were familiar ones to critics of the movement, Xenophon's speech brought to the widest audience possible a synthesis of the recent and not so recent claims against the leadership of Scientology, allegations picked up worldwide within minutes of him speaking.

He described claims of "false imprisonment, coerced abortions, embezzlement of church funds, physical violence, blackmail and the widespread deliberate abuse of information obtained by the organisation". At the centre of Xenophon's long, impassioned speech were the allegations of Aaron Saxton, who was "born" into Scientology and "rose to a position of influence in Sydney and the United States".

According to Xenophon, Saxton's abuse started as a child when his mother was coerced into signing over guardianship of him to the organisation and he was made a security guard at the age of 16. "In 1991 Aaron says he was sent to Scientology headquarters in Florida where he was involved in… putting five individuals under house arrest" and "ordered by superiors to remove documents that would link a Scientology staff member to murder".

"Aaron says women who fell pregnant were taken to offices and bullied to have an abortion. If they refused, they faced demotion and hard labour… Aaron says one staff member used a coat-hanger and self-aborted her child for fear of punishment. He says she was released from the organisation and the files were destroyed."

Saxton also "ordered more than 30 people to be sent to Scientology's work camps, where they were forced to undertake hard labour", Xenophon said.

He said another former Scientologist, Carmel Underwood, who worked as a financial officer in the organisation and claims to have been assaulted by another member, "witnessed a young girl who had been molested by her father being coached as to what she should say to investigating authorities in order to keep the crimes secret". In a letter described by Xenophon as "one of the saddest correspondences I have received", a father, Paul Schofield, admits to being part of a cover-up of the circumstances surrounding the deaths of his two daughters.

The Church of Scientology in Australia's response last week was to accuse Xenophon of abusing parliamentary privilege and adding that the allegations were "unquestionably false". "This was not free speech. It was abuse and slander protected by the forms of our parliament," spokesman Cyrus Brooks said in a statement. It did not, however, reply to a series of written questions from the Observer about the cases detailed.

But if something has changed in the past few years, it has been the emergence of an increasingly empowered and vocal global opposition to the Scientologists. The development has been fuelled in part by the internet's Anonymous movement – which posted the Tom Cruise video to YouTube last year – and has been behind a series of denial-of-service attacks on Scientology websites, protests and prank calls since the Scientologists had it removed it from the site, inevitably claiming copyright infringement. The Australian intervention by Xenophon was part of a wider and growing backlash against one of the world's most controversial movements.

If there has been a catalyst for many of the Scientologists' most recent problems it has been provided by a newspaper in Florida – the St Petersburg Times – which covers the area including the organisation's spiritual headquarters in Clearwater. The paper ran an investigative series featuring interviews with former members of the church's leadership. These included Marty Rathbun and Mike Rinder, two of the highest-ranking executives to leave Scientology.

According to the two men's accounts – denounced as "lies" by Miscavige and Tommy Davis – Miscavige routinely assaulted his lieutenants, including Rinder, 50 times. In one article, citing the testimony of four former members, the newspaper described Miscavige administering a vicious beating to another senior church figure, Tom De Vocht. The men described a complex system of internal justice, enforced by security checks and the threat of isolation as a so-called "suppressive person" or SP.

In the interviews the men admitted using violence against other members of the church, often, they claimed, at the behest of Miscavige, also alleging that the church used private information gathered on its members to bully them and force them to do its bidding.

At least some of the recent allegations will be familiar to Jason Beghe, the American actor. Last year he became the first of its celebrity followers – for whom the church maintains a "Celebrity Centre" – to break with it, after giving Scientology more than $1m in donations over 12 years.

These days Beghe prefers to warn that the church is "destructive and a rip-off". He claims that since his renunciation of Scientology he has been pursued to seminars in Europe – held to speak of its dangers – by private investigators employed by Scientology and "disconnected" from former friends who remain within it.

The decision of Beghe and Haggis to quit Scientology appears to have caused the movement its greatest recent PR difficulties, not least because of its dependence on Hollywood figures as both a source of revenue for its most expensive courses and an advertisement for the religion. The involvement of such high-profile figures as Haggis, Cruise and John Travolta has acted as a reassurance for potential recruits against the allegations of its critics.

And while Haggis quit the church over its attitude to gay marriage, his lengthy leaked letter of repudiation of Scientology, written to Davis, included another complaint: that he had lied on television about a key Scientology practice.

Haggis said he had been stunned to see a CNN clip of Davis denying that the church practises a policy of "disconnection" by encouraging members to cut ties with non-members who may disapprove of their beliefs.

"I was shocked," wrote Haggis. "We all know this policy exists. I didn't have to search for verification – I didn't have to look any further than my own home." He then detailed how his wife was ordered by the church to disconnect from her parents because they were themselves ex-members.

His wife followed the orders and did not speak to her parents for a year and a half. "That's not ancient history, Tommy. It was a year ago… To see you lie so easily, I am afraid I had to ask myself: what else are you lying about?"

The answer to that question may now be sought within the context of an Australian parliamentary inquiry. Notoriously litigious and undoubtedly secretive, Scientology is under the microscope again.

After a bad year for Cruise's church, things could be about to become a whole lot worse.

History of scientology

Founded by L Ron Hubbard (1911-1986), a science-fiction novelist who turned to pulp writing after a wartime military career marked by a number of disgraces. It was while writing for Astounding Science Fiction in 1949 that he published his first article on the subject of dianetics, which would later become Scientology. It was described by one critic as "a lunatic revision of Freudian psychology". His book Dianetics: the Modern Science of Mental Health was published in 1950. Attempts to set up dianetics as a therapeutic practice collapsed.

1952 Having failed to present dianetics as an empirically supported scientific system, Hubbard founded a religion called Scientology, which he claimed was the result of years of research. Using "e-meters" to "measure" the mind, he claimed it could be "cleared" by a process of "auditing". At this point based in England, he ran into problems with the authorities. He founded the Sea Organisation, or the Sea Org, which would become the movement's central group.

1970 Scientology establishes its celebrity centre in Los Angeles, aiming to attract Hollywood high flyers.

1977 Scientology runs into trouble in the US, this time for domestic espionage against the federal government, for which Hubbard's wife and a dozen other officials were convicted of conspiracy.

1986 Hubbard dies of a stroke in California.

1993 Scientology is declared tax-exempt as a church in the US, ending a 40-year battle.

1999 Refused tax-exempt status by the UK charity commission, which rules it is not a religion. However, in the years that follow it is recognised as a religion in a number of countries, including Sweden, New Zealand and Portugal.

2006 A repeat of a South Park episode that spoofs Tom Cruise and Scientology is pulled from the air.

2009 The church is found guilty of fraud in France. Screenwriter Paul Haggis splits with Scientology amid accusations of homophobia. Tom Cruise and John Travolta are still members of the Church of Scientology.

• This article was amended on Thursday 26 Novemeber 2009. We said that the St Petersburg Times was in Tampa, Florida, which is one of the areas it covers but is not where it is based. This has been corrected.