Religious Studies 'short' version, covers half the subjects and counts as half a GCSE, but has been removed from Department for Education performance tables.
The National Association of Teachers of RE (NATRE) said that was having a "serious and negative impact" on the number of pupils choosing to take the short course.
- 26.8% drop in RS short course entries
- 5.3% rise in RS full course entries
- 29.6% of entries for full course awarded A or an A*
It said there was an increasing number of schools having no pupils at all taking the subject.
Take up in England of the GCSE RS short course has fallen from 211,269 in 2012 to 68,890 in 2015, a drop of 67.3%.
But the number of teenagers taking the full subject was up by 5.4% to 271,917.
This echoes the increase in A Level entries in England and Wales, which are up 6.5% this year compared with 2014.
In 2014 there were 1,197 schools making no entries for any RS qualification, a rise from 268 in 2010.
NATRE said overall figures showed that compared with 2012 over 85,000 more pupils in England will complete key stage 4 with a qualification in Religious Studies.
Daniel Hugill, Chair, National Association of Teachers of RE, said: "Congratulations to the many students receiving their Religious Studies results today, and to their teachers who have worked tirelessly to ensure that their students can reach their full potential.
"GCSE in Religious Studies makes a key contribution to preparing young people for adult life in our pluralistic society and global community. It is clear though that not all students receiving their GCSE results today were offered the opportunity to study this important subject.
"The increasing number of schools that have not entered a single student for an accredited Religious Studies qualification is a grave concern.
"It is hard to see how these schools are ensuring a suitable degree of religious literacy in their students.
"NATRE will continue to call for a system that rewards schools for guiding students to study a combination of courses at 14+ that are in each individual's best interests and that will properly prepare them for life in the modern world.
"The current set of school accountability measures falls short of this aim."
Joyce Miller, Chair, Religious Education Council of England and Wales said: "I am heartened to see the rising number of entries for the GCSE full course in Religious Studies. This demonstrates the attraction of an academically rigorous subject that helps prepare students to understand an increasingly diverse modern world.
"However it is frustrating that this enthusiasm among pupils for RS is not being translated into entries for the RS short course due to it not being appropriately recognised in performance tables.
"It is alarming that in England there is an overall decline in pupils receiving a solid grounding in RE due to the dramatic fall in short course entries.
"The danger is that, as our society becomes increasingly multicultural and religious extremism continues to dominate the news agenda, we create a section of society that lacks an understanding of diverse faiths and beliefs that is essential to growing up in twenty-first century Britain."