The unnamed youth was served the summons by City of London police when he took part in a peaceful demonstration opposite the headquarters of the controversial religion in London.
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Officers confiscated a placard with the word “cult” on it from the youth, who is under 18, and a case file has been sent to the Crown Prosecution Service.
A date has not yet been set for him to appear in court.
The decision to issue the summons has angered human rights activists and support groups for the victims of cults.
The incident happened during a protest against the Church of Scientology on May 10.
Demonstrators from the anti-Scientology group, Anonymous, who were outside the church’s ?23m headquarters near St Paul’s cathedral were banned from describing Scientology as a cult by police because it was “abusive and insulting”.
Writing on an anti-Scientology website, the teenager facing court said: “I brought a sign to the May 10th protest that said: ‘Scientology is not a religion, it is a dangerous cult’.”
“‘Within five minutes of arriving I was told by a member of the police that I was not allowed to use that word, and that the final decision would be made by the inspector.”
A policewoman later read him section five of the Public Order Act and “strongly advised” him to remove the sign. Section five of the Public Order Act prohibits signs which have representations or words which are threatening, abusive or insulting.
The teenager refused to back down quoting a 1984 high court ruling from Mr Justice Latey, in which he described the Church of Scientology as a “cult” which was “corrupt, sinister and dangerous”.
After the exchange, a policewoman handed him a court summons and removed his sign.
On the website he asks for advice on how to fight the charge: “What’s the likelihood I’ll need a lawyer? If I do have to get one, it’ll have to come out of my pocket money.”
Writing on the same website, another anonymous demonstrator said: “We also protested outside another Scientology building in Tottenham Court Road which is policed by a separate force, the Metropolitan police, who have never tried to stop us using the word cult.
“We’re completely peaceful protesters expressing a perfectly valid opinion. This whole thing stinks.”
The City of London Police, who issued the summons, came under fire two years ago when it emerged that more than 20 officers, ranging from constable to chief superintendent, had accepted gifts worth thousands of pounds from the Church of Scientology.
City of London police chief superintendent, Kevin Hurley, praised Scientology for “raising the spiritual wealth of society” during the opening of its £23m headquarters near St Paul’s Cathedral in 2006.
And last year a video praising Scientology emerged featuring Ken Stewart, another of the City of London’s chief superintendents, although he is not a member of the group.
The group was foundeded by science-fiction writer L Ron Hubbard in 1952 and espouses the idea that humans are descended from an exiled race of aliens called Thetans.
The church continues to attract controversy over claims that it separates members from their families and indoctrinates followers.
A spokeswoman for the force said today: “City of London police had received complaints about demonstrators using the words ‘cult’ and ‘Scientology kills’ during protests against the Church of Scientology.
“Following advice from the crown prosecution service some demonstrators were warned verbally and in writing that their signs breached section five of the Public Order Act.
“One demonstrator continued to display a placard despite police warnings and was reported for an offence under section five. A file on the case will go to the CPS.”
The decision by City of London Police to issue the summons provoked anger from civil liberties campaigners and groups helping former cult members.
Liberty director, Shami Chakrabarti, said: “This barmy prosecution makes a mockery of Britain’s free speech traditions.
“After criminalising the use of the word ‘cult’, perhaps the next step is to ban the words ‘war’ and ‘tax’ from peaceful demonstrations?”
Ian Haworth, from the Cult Information Centre which provides advice for victims of cults and their families, said: “This is an extraordinary situation. If it wasn’t so serious it would be farcical. The police’s job is to protect and serve. Who is being served and who is being protected in this situation? I find it very worrying.
“Scientology is well known to my organisation, and has been of great concern to me for 22 years. I get many calls from families with loved ones involved and ex-members who are in need of one form of help.”