The Commission on Religious Education has also called for a 'national entitlement' - or a minimum level of RE provision - for state-school pupils.
Chair of the commission, Very Rev John Hall told Premier: "There are quite a large number of schools where there is no effective religious education taught, certainly at Key Stage 4 for children in their years up to 16.
"Forty per cent of academies without a religious character do not offer religious education at Key Stage 4."
The Commission called for dedicated teaching time and resourcing for teachers to enable them to do Religious Education "well".
RE faces "a perilous future without strategic, urgent intervention", the body - which comprises of education experts and academics among others - warned.
The Commission said the subject faces multiple pressures, including a fall in RE exam entries, more people identifying as non-religious and "inconsistency" in the quality of lessons.
In the new report, it concluded: "We are advocating RE for all not because children belong to religious traditions or not, but because in our age a nuanced understanding of the role of worldviews must be a part of citizens' intellectual make-up."
The Commission for Religious Education also recommended requiring schools to publish details of how they will meet the proposed national entitlement.
RE is currently compulsory in state-funded schools throughout England and schools decided how to teach the subject, whether through specific classes or alongside others.