Critics fear the policy could further diminish the number of students taking Religious Education, as a result of being left out of the EBacc.
The new system, first introduced in 2010, measures pupils with GCSEs in five subjects. These have to be good passes (A* to C) in English, maths, a language, two sciences and either geography or history.
The National Association of Teachers of Religious Education (NATRE) has said that in schools where entry levels had fallen, more than half or RE teachers blamed the impact of the introduction of the Baccalaureate.
The Bishop of Portsmouth, Rt Revd Christopher Foster, said the decision not to make RE a compulsory subject "hugely disappoints" him.
The religious dimension to life, the understanding that the spiritual is at the heart of who we are as men and women and children made in God's image and likeness; the importance of that needs to be recognised in every facet of our community life," said Bishop Christopher to Premier.
Learning to be sensitive to that is part of a rounded and proper education," he added.
The Government believes that a compulsory EBacc will enhance the prospects of pupils, particularly disadvantaged pupils, by ensuring they receive a respected core academic curriculum that allows them to retain options in subsequent education and in the employment market.
Concerns have also been raised that the EBacc may not be suitable for a significant number of pupils, and that teacher supply, particularly in languages, could pose problems for implementation.
