Under new rules that come into force in September, voluntary controlled schools will be allowed to reserve a head's post for someone with religious views in line with the school's faith. The Government is consulting on transitional arrangements that would ensure heads already in post will be protected.
But the society says the safeguards are discriminatory as they do not extend to other teachers at the schools who may have been in line for promotion in future.
The Department for Children, Schools and Families said it was considering all responses.
Keith Porteous Wood, the society's executive director, said: "The Government has ignored our pleas to protect the thousands of teachers in voluntary controlled schools who have some prospect of promotion to a headteacher post. The law has been changed to enable headteacher posts to be reserved for teachers with a degree of piety that few will be able to muster.
"Natural justice demands that teachers in post before this change should not be affected by it. The department is giving the impression that current staff are protected, but the small print shows they are not."