The decision, won by a law team led from East Grinstead, could mean the Charity Commission will have to recognise the controversial Church of Scientology as a bona fide religious group.
This would give it access to a series of tax breaks and potentially hundreds of thousands of pounds in taxpayers’ money through Gift Aid.
The European Court ruled the Russian government should be forced to recognise the Church as a religious organisation.
But if the decision is rolled out across the EU the group, which is viewed as a business in many countries, could save millions of pounds.
The UK headquarters of the Church of Scientology is in East Grinstead and has been visited by Tom Cruise, the creed’s most high-profile follower.
The organisation was turned down for charitable status in 1999 because the Charity Commission ruled scientology was not a religion in English charity law.
Graeme Wilson, the director and spokesman for the Church of Scientology in England and Wales, said it had not decided whether to reapply.
But he said some UK bodies had already recognised scientology as a religion, including the City of London last October when it granted the Church charitable rates relief.
He said: “Over the years there have been many official recognitions of scientology’s religiosity throughout Europe, including in Britain.
“This latest decision sets a Europe-wide precedent and will help to resolve any remaining areas of discrimination against religions in Europe.”
The Church, founded by American science fiction writer L Ron Hubbard, claims to have 123,000 UK supporters. There are scientology churches at Saint Hill Road in East Grinstead and at North Street in Brighton.
Mr Wilson said: “The vast majority of people are recognising this is mainstream. It is in over 160 countries around the world, with 7,000 churches and different organisations.”
The court application was led by East Grinstead lawyer Peter Hodkin and won under Article 11 – the freedom of assembly and association – of the European Convention on Human Rights read in the light of Article 9 – the freedom of thought, conscience and religion.
The court ruled that the Church of Scientology had been “discriminated against as a religious minority” and “was restricted in exercising the full range of its religious activities”.
The group was partly refused charitable status in 1999 on the grounds that it was not “established to promote the moral or spiritual welfare or the improvement of the community”.
It has since established an anti-drugs campaign with schools and the police in the UK using scientologist swing band Jive Aces to front the message and a “youth for human rights” campaign.
A spokesman for the Charity Commission said it was not yet clear whether it would change its view in light of the court decision but it was open for the Church to reapply.
He said the convention had been taken into account by commissioners at the time.
A registered charity does not normally pay income or corporation tax, capital gains tax or stamp duty. It has reduced business rates and can raise money from local government more easily. Legacies are not liable to inheritance tax and where donations come from taxpayers, the charity can claim 28 per cent extra from the Inland Revenue.