Ruth Kelly, the Cabinet minister responsible for equality, is said to be at odds with Peter Hain, the Northern Ireland Secretary.
The rift is due to Mr Hain pushing through regulations in the province outlawing discrimination against gays, lesbians and bisexuals.
The regulations which take effect in Northern Ireland on 1 January, are tougher than Ms Kelly’s plans for England, Wales and Scotland.
Mr Hain has defied a call by Ms Kelly to hold fire until a common approach has been agreed.
Gay rights campaigners are urging Ms Kelly to extend the Northern Ireland rules to the rest of the UK, but church leaders are urging ministers not to put the rights of gays above the rights of Christians.
Colin Hart, director of the Christian Institute said: "Peter Hain talks about equality. But he should read his own regulations, which elevate gay rights above all other rights for religious people, and rights on the grounds of age, sex and disability. It is a preferential status which will drive a coach and horses through religious liberty."
The new Commission for Equality and Human Rights will have the power to intervene without receiving a complaint of discrimination.
Anglican and Catholic churches could be sued if their bookshops refuse to stock gay literature and hotel owners with strong religious beliefs could be fined if they do not allow gay couples to share a room.
Q. Should England, Wales and Scotland adopt the same tough regulations outlawing discrimination as those set to be implemented in Northern Ireland?
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