Rev Gavin Ashenden, who is also a former chaplain to the Queen, made the comments following Mark Bonney, the Dean of Ely revealing that the cathedral would join others marking the start of the city's new Pride Festival.
In a statement sent to Premier, Rev Bonney said: "I am very pleased that Chapter agreed to my request to fly the 'Pride' flag from the Cathedral tower on 11 August when Pride in Ely holds is first festival. I am pleased first of all to lend my backing to this community event because it celebrates the breadth and diversity of the community in which we all live.
"I am also very conscious that Christians have not always been perceived as being as supportive and inclusive as some of us would wish, and so I am pleased to fly this flag as a sign of the kind of inclusion that I wish to promote at the Cathedral."
In a blog post, titled 'Ely cathedral and the great apostasy', Rev Ashenden said: "The Dean of Ely has adopted the secular values of a culture that has set its face against Christianity, and is waging a war against Judaeo-Christian culture. Sexual ethics have always been at the heart of the Christian's struggle with sin, the world and the devil. But it seems the Dean of Ely is not over concerned with either sin, or the distinction between the Church and the world, or the struggle with evil.
"But then more and more cathedrals see themselves as civic centres of spirituality, wanting to embrace the secular. Jesus warned that you could not more serve God and mammon than you could submit to the temptations of the devil and still work for the Kingdom of Heaven.
"In the case of Ely, the Dean is choosing the Leftist values of so-called 'breadth and diversity' (values found nowhere in the Christian Gospels) and wants to make reparation for the fact that Christians have been insufficiently supportive of non-monogamous and heterosexual sexual adventure (code word 'inclusivity'- another term found nowhere in the teaching of Jesus.)"
The rainbow flag will be put up on Saturday.
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