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The Government does not routinely monitor compliance with equality legislation of any particular body or organisation, including the Church of England.
It would be a matter for an individual who felt that they had been discriminated against by the Church, or any other religious organisation, to seek a resolution including, ultimately, bringing a case to the courts.
In order to help assist in informal resolution of any situation, members of the public who feel that they have suffered discrimination because of religion or belief, or any other protected characteristic, can contact the Equality Advisory and Support Service. That is a free service covering England, Scotland and Wales which offers advice on dispute resolution, prior to consideration of instigating formal proceedings.