Faith schools are being created "by the back door" as religious groups bypass rules on school competitions, it has been claimed.
The Government has given the Church of England approval to take over two community schools without giving non-religious organisations the opportunity to compete.
Grange View First School in Widdrington, Northumberland, is closing down as a community school and will reopen as a CofE school next month.
Bourne Abbey Primary in Lincolnshire will also make the switch.
A third school has won exemption to change its religious character without going to a competition, it is understood, but no further details are available.
The changes were made possible after the Department for Children, Schools and Families gave the schools special exemptions from competing with other providers.
These decisions come in spite of rules that call for all new schools - which include those changing their religious character - to be decided by a competition, allowing charities, local authorities and other organisations to make bids. The aim is to break-up the traditional structure of state education.
But Andrew Copson, education director of the British Humanist Association, said: "The Government claims they do not force religious schools on communities, but this flouting of their own rules shows otherwise. Special permissions are being given for the conversion of community to religious schools, but it is almost impossible to open a new inclusive community school.
"This is a deeply worrying trend of state-funded religious schools by the back door. It will lead to a lack of choice for parents."
Since the rules were introduced, no school that has changed from being a community to a faith school has gone to a competition.
Northumberland County Council said it approved the change at Grange View because it would help attract pupils that might otherwise go to a religious school in a neighbouring village. Closer links with the church would also enhance pupil wellbeing, the council said.
But concerns were raised about parental support for the change and its potential impact. In a letter approving the competition exemption, the DCSF said that Ed Balls, the Secretary of State, would have liked more evidence of parental backing for the switch.
It added that he would have liked greater explanation of how the change would raise standards.
Seven community schools in Northumberland have become CofE schools in the past five years.
A spokeswoman for the DCSF said the views of parents and the effect of changes on school diversity were taken into consideration before granting an exemption.
The move comes as voluntary controlled schools are given new powers to reserve headships for followers of the faith of the school.
Heads already in post will be protected, but critics argue the change could disadvantage thousands of teachers seeking promotion to headship.