Rt Rev John Pritchard, who chairs the Church's education board, said "very short notice" changes were "not the best way to build for the future".
He expressed concern about support for Church-run academies and the exclusion of RE from the English baccalaureate.
The government said RE was important and remained compulsory.
"The changes brought in by the present Coalition government present significant challenges to the Church' s continued involvement in the public education system," Rt Rev Pritchard wrote in a report to General Synod.
"The changed rationale and growth of academies requires action now to ensure the survival of our provision."
The rapid pace of change was "not the best way to build for the future", he said.
The Bishop of Oxford said there were "serial challenges" to the "national well-being" of religious education in non-faith schools.
The exclusion of the subject from the English Baccalaureate had had an "immediate and depressing effect" on the GCSE choices pupils were making nationally, he said.
The Ebacc is awarded to students who get good GCSE passes in English, maths, two science qualifications, a language and history or geography, and is already one of the measures used to rank schools in league tables.
He said standards in RE were "not healthy" and teaching about Christianity was "generally not well done".
Even the Church of England's own schools should not be "overly complacent" about their teaching of Christianity, he wrote.
The Department for Education said RE was an "important part of the curriculum - that is why it remains compulsory".
The English Baccalaureate is "about ensuring pupils from all backgrounds have the chance to study a core of the main subjects, including those such as languages and history where entries have declined in recent years in a number of schools", a spokesman said.
Success in the RE GCSE will continue to be recognised by other school performance table measures and as a qualification in its own right, the spokesman added.
Faith-based placesRt Rev Pritchard also said "hostility towards faith-based schools" had increased, with "renewed attacks" on the principle of reserving places for children who attend church.
The Bishop said earlier this year that he believed up to seven in 10 Church of England schools could become academies in the next five years.
The report points out that already, with at least 42 academies, the Church of England is the largest single provider of academy schools.
But it says only "a very small number" have places which will be allocated on the basis of religious observance.
The bishop warned that there had been a danger that Church of England schools that became academies could "let the Church foundation drift until it had no meaning".
This had been averted by the production of Church guidelines for new academies, he said.
But dioceses would increasingly need to develop ways to support schools in the way that local authorities currently do, for example by managing "poor performance" in Church schools, he said.
The Church of England has around 4,700 schools educating almost a million children.
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