Schools are at risk of "infringing the rights of children, parents and teachers" to practise their religious beliefs, the Christian Institute has warned.
The warning comes following an independent Christian school being told it may be rated just "adequate", rather than its current "good" status, by Ofsted inspectors.
The school is accused of "not promoting other faiths," deputy director of the Christian Institute, Simon Calvert, said.
"Astonishingly it was told it should invite representatives of other faith groups to lead assemblies and lessons, such as an Imam," he added.
Calvert said this is evidence of new regulations, established in the wake of the Trojan Horse scandal, "requiring Ofsted inspection teams to behave in ways which do not respect the religious ethos of faith schools".
"The wording of the regulations inevitably results in these kind of outcomes. While we obviously support attempts to address the problem of radicalisation, the current regulations fail to do this," he said.
According to the Telegraph, the Christian Institute is providing legal support to the school, and has outlined its concerns in a letter to Education Secretary Nicky Morgan.
It lambasts the "disturbing consequences" that the new regulations are having on faith schools.
However, an Ofsted spokeswoman told the Telegraph that a "broad and balanced education" in British schools is vital.
"Inspectors will consider the effectiveness of the school's provision for pupils' spiritual, moral, social and cultural development and how the school's leadership and management ensure that the curriculum actively promotes British values," she said.
"This includes, among other factors, pupils' acceptance and engagement of different faiths and beliefs, and their understanding and appreciation of the range of different cultures within school and further afield."
Former Prime Minister Tony Blair last week urged schools across the globe to teach "the virtue of religious respect".
In an article for the BBC News Knowledge Economy series, Blair argued that "education is a security issue", and without a commitment to fostering respect and understanding between children of different faiths, we risk "worsening ideology in the long term".
"This should be a common global obligation...Nations should feel the pressure to promote respect and to eradicate disrespect," he said.
In the wake of the Christian Insitute's latest claims, the Chair of the National Association of Teachers of RE (NATRE), Ed Pawson, has also leant his support to encouraging diversity in religious education.
He told Christian Today that "Young people growing up in Britain today are entitled to learn about the rich and diverse religious and cultural communities which make up our world."
"I am delighted to read the comments of Nicky Morgan, the Education Secretary, who says that schools should encourage children to learn about 'lots of different ideas and learn to be tolerant of other faiths and beliefs'," Pawson continued.
"Whether children are in a faith school or community school they have a right to know about beliefs and worldviews other than their own, and all schools have a duty to open the eyes of their pupils to the amazing variety of different believing communities in society today.
"Surely, religious tolerance and understanding is an ethic that underlies all the great religious traditions? How can learning about each other be seen as harmful to our young people?"
The Christian Institute did not respond immediately to a request for more information on this particular case.