Secular campaigners claim new legislation threatens teachers' jobs by allowing the Church of England to strengthen its power over thousands of schools and discriminate in favour of church-going staff.
They are concerned about what will happen if more than 2,500 religious schools which currently have voluntary controlled (VC) status follow ministers' wishes and convert to academies.
Religious VC schools can currently only insist that a fifth of their teachers are religious. But that could change because of the Education Bill, debated in Parliament for the first time this week.
If the VC schools became academies, the bill says the education secretary could agree to the churches behind them having greater power to discriminate in favour of teachers and other staff who are religious.
They would, like voluntary aided (VA) schools, be able to give preference - in terms of appointments, pay and promotions - to those whose "religious opinions" match the school, who "attend religious worship" and who are prepared to teach in accordance with the school's religion.
The Government says the purpose of the clause is merely to allow academies to mirror the switch from VC to VA that church schools can already make with the secretary of state's permission.
But the National Secular Society says academies run by churches are much more likely to want greater control over staffing than VC schools where local authorities still have an influence on the governing body.
The vast majority of VC schools are Church of England primaries, many in rural isolation, and the society argues the bill could damage prospects for teachers in such areas.
"After decades of plunging church attendance, it is outrageous that control of often the only publicly funded school for miles will be passed to a religious group," said Keith Porteous Wood, the society's executive director.
"The likelihood is for the converting schools to become much more religious. And if the secretary of state exercises the power he seeks, religious teachers could increasingly get preference over better qualified non-religious ones, whose local re-employment options could be severely reduced."
The society also points out that while a VC school has to consult to gain VA status, there is no requirement in the bill for a former VC school to consult over acquiring new staffing freedoms once it has converted to an academy.
But the Department for Education says permission for the staffing changes would only be given "where an academy has consulted upon, and received widespread support for, a change from a minority to a majority church representation on the academy trust".
A Church of England spokesperson said: "All the bill does is appropriately carry forward conditions which applied in voluntary schools into academies. Nothing has fundamentally changed."
The secularists fear the Church will seize any opportunity to win greater control over staffing, pointing to guidance it issued in 2008 advising its VC schools to use a change in the law to ensure that future heads were religious.
But the DfE said: "In church schools, we have always wanted to ensure that on (academy) conversion, the levels of religious staffing should remain the same."