The Church Times reports this week that ministers are still considering a report from the Qualifications and Curriculum Authority, which has already been with the Department for Education and Skills for seven months.
There are fears that political sensitivities have delayed or derailed the framework, according to the Church of England's newspaper.
RE is compulsory although it is not in the national curriculum. At present its content is determined locally, by standing advisory councils set up by local authorities. Sacre members at a QCA conference on Monday expected to hear new national guidelines had been approved. Instead, a DfES statement said it was still being considered.
It said Mr Clarke was "aware that issues in RE are sensitive and that a framework could be a useful tool to deal with some of those sensitivities" but added that the DfES needed to look beyond that.
The Church Times says RE leaders believe the statement sounds the death-knell for a national framework and they were said to be "incandescent".
The RE Council of England and Wales immediately expressed its "dismay and frustration". It says there is widespread support for a national framework to raise standards and promote the subject's status in schools.
Dr John Gay, C of E spokesman on RE, said: "We are very disappointed. We have always supported this initiative which we believe is essential for the future of RE."
The Rt Rev Alan Chester, Bishop of Blackburn and Canon John Hall, chairman and general secretary respectively of the Church's board of education will raise the issue with minister Cathy Ashton next week.
A QCA spokesman said the authority had already invested "a lot of work" in a draft non-statutory framework. It completed a study in March, which found a consensus in support of a national curriculum style booklet to help "promote consistency and quality" and develop the subject. Findings were accepted by the QCA and submitted to the DfES as advice.