Communities Secretary Eric Pickles said a majority of the public didn't want the "controversial organization" to receive the kind of favorable treatment usually reserved for charities, The Guardian reported.
It is the first time a Cabinet minister has intervened in long-running arguments over tax breaks for Scientology, which a high court judge classified as a cult in 1984, the report said.
The tax breaks are costing localities millions of dollars in revenue, and at least four authorities, including the city of London are among the entities granting the cuts.
The City of London Corp. asked Scientology to pay just 20 percent of its usual tax rates on its London headquarters; as a result it saved more than $1 million in taxes.
Pickles said he doesn't understand why Scientology is given privileged treatment.
"Tolerance and freedom of expression are important British values, but this does not mean that the likes of Church of Scientology deserve favored tax treatment over and above other business premises," Pickles told The Guardian.