Religious education lessons for 14 to 16-year-olds have been scrapped in one in four schools despite being obligatory.
Most of the schools that have dropped the subject say it is because it does not count towards the new English Baccalaureate.
Education Secretary Michael Gove provoked anger when he announced History and Geography were the only humanities subjects that would count.
Ed Pawson, chairman of the National Association of Teachers of Religious Education, called his decision "truly... a cruel blow". RE is a compulsory lesson but does not have to be taken at GCSE. It was one of the fastest-growing GCSEs after 9/11 as pupils grew more interested in religions.
But the numbers who have chosen it this year in academies and community secondary schools are down by a third since last year.
Under present proposals, pupils would qualify for an English Baccalaureate certificate if they obtain five A*-C grades in Maths, English, Science, a foreign language and a humanities