Staff and students are "not to be undermined" at Church of England schools for their views on gender and sexuality, a senior Church official said on Friday.
Stephen Conway, the Bishop of Ely and chair of the National Society - the Church of England's educational body - said that schools had certain duties in light of faith being a protected characteristic under British law.
"All schools are bound to make sure that students, staff, governors are all safeguarded and not to be undermined if they take a particular view from a Christian perspective," he told the Church of England General Synod on Friday,
"There's no way in which the National Society can monitor this too closely but all schools are bound to provide this protection for every member of the community."
Questions have arisen over the Church's stance following the controversy surrounding the resignation of John Parker as a C of E school governor over its handling of a child's transition.
He said that the Bishop of Chelmsford had told him that his "biblical views on sexuality were not welcome in the Church of England" and that he could "leave" - accusations that the bishop has repeatedly denied.
Explaining the reasons for his resignation, Mr Parker expressed concern at the school's decision to bring in controversial transgender lobby group Mermaids to do a staff training session.
On Friday, Synod member and conservative evangelical blogger Ian Paul asked why the Church of England had included Mermaids in the 'helpful resources' section of 'Valuing All God's Children', its policy document on eradicating homophobic and transphobic bullying in its schools.
"Given the really serious criticisms and problems that have been raised about some of the guidance in schools, including errors of fact, the ignorance of science, and even in some of the material, recommendations that actually breach good safeguarding practice, at what point might the education office actually offer more direct and positive guidance in what for many schools is a really complex and important area, but an area in which many people feel very fearful about making decisions?" Mr Paul said.
In response, Bishop Conway said that forthcoming guidance from the National Society on Relationships and Sex Education, which is becoming mandatory in English schools in 2020, would provide "clearer" guidance and support for schools in this area.
He said that 'Living in Love and Faith', the ongoing dialogue process in the Church of England on gender and sexuality, would "help us move forward with this".
"I fully understand the fact that people feel nervous about it," he said.
Mermaids was removed from 'Valuing All God's Children' following complaints that the Church of England appeared to be endorsing the organisation.
The bishop said that by including organisations in the 'helpful resources', the National Society was not recommending any of them "but only providing a picture of what resources might be available".
"It's for local schools and their governing bodies which, if any, provider they would choose to use," he said, adding, "It's a very fast-changing environment."