Westminster, the City of London and Camden Council have been urged to scrap 80% rate relief on Church of Scientology buildings.
The Church of Scientology Religious Educational College Inc. is believed to have saved nearly £2m from commercial rate breaks in the capital - in 2008 the non-for profit organisation filed an income of almost £13m.
Communities Secretary Eric Pickles said voters do not want to see preferential treatment of an organisation the Charities Commission refused to designate a church for tax reasons.
The Church of Scientology says local council authorities have "recognised the religious nature of Scientology".
Figures published in Private Eye revealed the full extent of how much the American based group benefits from rate relief.
The City of London saved the organisation £1.3m in rates on their London Org (centre) at Queen Victoria Street since 2006.
Westminster City Council has spared the group over £150,000 on its "London Celebrity Centre" in Leinster Gardens in more than a decade. The council classes the Church as a "non-registered charity" as it is "beneficial to the community,"
However, Camden Council have so far refused to reveal the discount it offers on the Scientologists "Stress Test Centre" on Tottenham Court Road.
Not all local authorities give the tax break, Manchester City Council and Mid Sussex District Council both charge the full commercial rate
Mr Pickles said: "Tolerance and freedom of expression are important British values, but this does not mean that the likes of Church of Scientology deserve favoured tax treatment over and above other business premises.
"The Church of Scientology is not a registered charity, since the Charity Commission has ruled that it does not provide a public benefit. Nor are its premises a recognised place of worship.
"Councils may award charitable relief. They should take into consideration the Charity Commission's rulings when weighing up whether to do so.
"I do not believe the majority of the public would want their own council to be giving special tax breaks to such a controversial organisation."
A Church of Scientology spokesman told the Guardian:
"Scientology is very popular with those who have visited our churches, met with Scientologists and observed or utilised our numerous community activities that effectively address drug abuse, illiteracy, declining moral values, human rights violations, criminality and more.
"Local council authorities, government bodies in this country and many others, and the European Court of Human Rights have all recognised the religious nature of Scientology, or the fact that Scientologists are actively helping those in their communities as a direct reflection of their religious beliefs."