The Board of Deputies is disappointed at the government's decision not to include religious studies as part of English Baccalaureate, or EBacc, its new performance measure for schools.
To qualify, pupils must gain GCSEs in five specified subjects - maths, English, science, geography or history and a foreign language.
The Board had joined religious and education organisations in lobbying for religious education to be counted towards the EBacc.
A Board spokesman described the government's decision as "a shame but not unexpected". A stronger view was voiced by Brian Gates, chairman of the Religious Education Council of England and Wales, who said: "It is now clear that current government policy is knowingly undermining religious education in our schools.
"Not including GCSE RE as a mainstream humanities subject in the 2010 English Baccalaureate has already resulted in many schools simply not offering it as a GCSE choice."
Earlier this year, deputies had been asked to raise the issue with their MPs by the Board's education and policy manager Hannah Ashleigh.
It was "of concern for the Jewish community", she wrote, "as in the vast majority of Jewish schools GCSE RE [Jewish studies] is a compulsory subject for all students.
"This means that our schools would be at a particular disadvantage when offering the EBacc if one of the subjects studied by all of their GCSE pupils did not count towards their achievement."
The omission of religious education, she added, would "also impact on the way in which young people in all schools across the country learn about Judaism, a vital tool in building understanding of our faith and traditions in wider British society".