Scientologists said they would appeal the decision, announced by the Charity Commission, which regulates charities in England and Wales.
The commission said the church did not meet the essential test for charitable status, "that of conferring public benefit." It said Scientology activities "were private in nature and in the benefit they delivered."
Graeme Wilson, public affairs director for the Church of Scientology in Britain, called the decision "wrong on the law and wrong on the facts."
"If the same logic were broadly applied, several hundred recognized charities in the U.K. would be deprived of their status, among them minority religions such as Buddhists, Jainists and Mormons," he said.
Some 187,000 charities are registered with the commission, including many associated with religions, both mainstream and otherwise. Registered charities receive tax benefits.
The Church of Scientology, which says it has 100,000 adherents in Britain, has not seen the sort of friction with the British government that it has seen in other European countries.
The German government has kept the organization under surveillance as a security risk and refuses it religious status. The Scientologists accuse Germany of religious persecution.