Religious leaders have attacked the Government for "sneaking out" a decision not to include RE in the English Baccalaureate, following a vociferous campaign for the subject to count towards the measure.
Ministers made a "wilful attempt" to prevent discussion by publishing their verdict at the end of the parliamentary and school year, according to the RE Council, which represents groups including the Church of England, the Catholic Church and the Muslim Council of Britain.
Education secretary Michael Gove said at the beginning of the year that he would listen to arguments to include RE in the EBac.
But ministers' decision last week to stand by their original decision to exclude the subject is "knowingly undermining RE in our schools" and causing it "serious collateral damage", according to the RE Council.
The backlash came as the Commons education select committee published a critical report into the EBac, which also called for the subjects that are included in it to be reviewed. To achieve the measure, pupils must achieve A*-C GCSEs in English, maths, geography or history, two sciences and a foreign language.
Graham Stuart, the Conservative chairman of the education select committee, said. "Our inquiry uncovered significant concerns about the EBac's composition, (its) potentially negative as well as positive impact, and the way it was introduced.
"We received a huge amount of evidence and the Government needs to look at that very closely; indeed, if it had conducted a similar consultation, it might have avoided some of the concerns which have been expressed."
The select committee report said the exclusion of RE had "perhaps been the most hotly contested aspect of the award's introduction", and had been opposed by more than 100 MPs.
Religious leaders also criticised the policy following its announcement at the end of last year, warning that it would see resources diverted away from RE and into EBac subjects.
A survey by the National Association of Teachers of RE last month showed that a considerable number of schools have already squeezed the amount of time given to the subject.
RE Council chairman Brian Gates said: "Despite the representations and clear arguments made for including RE, the Government has decided to dig its heels in.
"To sneak it out at the end of the parliamentary session and the end of the school year was extraordinary. It suggests a wilful attempt to prevent it getting in the public domain too quickly. It was the last possible time for MPs being around to speak up."
Oona Stannard, director of the Catholic Education Service for England and Wales, said that the way the government decision was released was "very strange".
"There was not an overt statement with an explanation for their reasons, and the timing seems very odd coming before the select committee report and at the end of the school term," she said.
"It did not leave the opportunity for people to discuss and respond to it, and it could not have been properly informed by the select committee report."
The Right Reverend David Rossdale, Bishop of Grimsby and vice-chair of the CofE's board of education, described the timing of the decision as a "surprise" and said that not supporting RE showed a "lack of joined-up thinking in Government" as it attempts to tackle religious extremism.
Elsewhere, the education committee's report said the EBac risked "shoe- horning" pupils into taking inappropriate qualifications.
Shadow education secretary Andy Burnham said: "We are already hearing that RE, music and art teachers are being made redundant," he said.
"It begs the question - what has this Government got against creativity?"
But schools minister Nick Gibb said that pupils from poorer backgrounds were considerably less likely than their more affluent peers to take EBac subjects
"These academic subjects reflect the knowledge and skills young people need to progress to further study or to rewarding employment," he said.
"The EBac is not compulsory but it is about closing the attainment gap between rich and poor and about increasing opportunity."