John Parker, a clergyman in the Diocese of Chelmsford, recently left his position as a school governor at a C of E primary school because of the school's handling of a child's gender transition.
A child in the school changed gender and members of staff and the school governors were given training by the organisation Mermaids, who said gender was like a dimmer switch and not an on-off light switch.
Rev Parker was unhappy that the matter was not discussed in advance of the transition and that he felt there had been no time made for talking about safeguarding nor the morality of it in a Christian school.
He said in a statement a week ago that leaving was his own decision but also suggested the Bishop of Chelmsford had implied he should leave the denomination.
Rev Parker wrote: "This situation, in its entire disregard for the Christian children and parents in the school, and those of other faiths and philosophies, presented the clearest possible instance of what Bishop Stephen had previously told me - that my Biblical views on sexuality were not welcome in the Church of England and that I 'could leave'".
On Tuesday, Rt Rev Stephen Cottrell issued a statement saying: "John Parker and I have always had a warm relationship and I was sad to receive his letter or resignation. I certainly did not, as has been claimed, ask or imply that he should leave the Church of England on account of his views on the matter in question, or that he was not welcome.
"Apart from anything else, I could not have done so because until I received his letter of resignation, I had no meeting or exchange of any sort with John since September 2018, nor did he ask for this."
"Additionally, at no point either before, during or after the episode in question did John contact the Diocesan Education Department about his concerns, nor did he ever meet with, correspond or request a meeting with the Director of Education."
The Bishop added that he supported the action of the Board of Education at the school and that they had "done right by the child". He said he respects the views of others and will continue to work with school about their use of external training providers.
He went on to say he did not want to exacerbate the issue but to reassure people that the priest had not been forced to leave and that he believes "it is possible for us to live together with our disagreements on these issues".
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