The Church of England has voiced concerns religious education is being sidelined by the government's school reforms.
The subject is facing "multiple challenges" but the government has "no will" to address them, the Anglican Church argued.
A new report on church schools warns that the government's responses to Christian leaders' concerns about RE have been "disappointing".
It says that the new English Baccalaureate has had a negative impact on the numbers of students taking RE and that excluding the subject from the current revision of the national curriculum is likely to have a "damaging effect" on its status.
The report also raises concerns about funding cuts, and reductions in training places for RE teachers.
"The teaching of religious education is subject to multiple challenges across the schools system that the Government seems to have no will to address," the report says.
It adds: "While the Church of England has received some encouragement to work together with other partners to address some of the issues related to religious education, the responses of the Government to these concerns have been disappointing.
"Realistically, the Church is limited in its ability to influence practice in the classroom even in its own schools.
"It does, however, have a voice and will continue to press for recognition of the damage being done to religious education."
Dr Priscilla Chadwick, chair of the Church School of the Future review group, said: "There is a danger that curriculum reforms emphasise a utilitarian philosophy of education, and the moral and spiritual aspect of educating the whole person could be pushed to the back, pushed to one side and in church schools that will not happen."
She added: "Pressures to teach to the test of the league tables, that governors and schools have to deal with, will not go away with the current government."
Chadwick said that schools were happy to be accountable, but added: "This pressure of a utilitarian approach to education is increasing with the current government.
"Church schools always pride themselves on their success and governance, but it can't be at the expense of real learning and nurture of the child."
The government's new EBacc is awarded to teenagers who score at least a C at GCSE in English, maths, science, a foreign language and a humanities subject, which has been limited to history or geography.
The exclusion of RE created a storm of protest, with campaigners arguing the move could see the subject marginalised in schools.
The Church of England's new report examines the changing role of its schools in England's education system.
It says that at a time when more schools are becoming academies, and free schools are being established, the Church should look to create new partnerships and provide the services that in the past were offered by local councils.
The Rt Rev John Pritchard, Bishop of Oxford, who leads on education for the Anglican church, said: "The entire educational landscape has shifted with many more types of school and different providers involved in a new market place.
"This is an opportunity and I would not be surprised to see at least 200 more Church schools developed in the next five years."
The Anglican Church is currently responsible for more than 4,800 schools, educating more than a million pupils.
A Department for Education spokesman said: "We make no apologies for bringing in the EBacc - it's a national scandal that tens of thousands of students don't enter GCSEs in core academic subjects like science, languages, geography or history after 11 years of taxpayer-funded education.
"By law every student still has to learn RE up to 18. The EBacc does not stop any school offering RE GCSEs. It is rightly down to schools themselves to make sure pupils take the exams right for them and decide how much teaching time to devote to RE - not politicians in Whitehall."