In an open letter to the Qualifications and Curriculum Authority, which drew up the guidelines, the National Secular Society said it was concerned that they "do not specifically require discussion of negative cultural attitudes to women often reinforced by religion".
The letter adds that the draft does "not require discussion of religious and cultural attitudes to homosexuality - often reinforced by religion, and their role in fostering homophobia".
The guidelines set out how RE should be taught to children aged three to 19, but it is up to individual schools what use they make of them.
They say Christianity should be studied at each key stage, while Britain's other principal religions - Buddhism, Hinduism, Islam, Judaism and Sikhism - are studied across the key stages. The guidelines also say that other religious traditions such as the Baha'i faith should also be addressed along with non-religious beliefs such as humanism.
The secular society also called for RE to be split from moral education so that children withdrawn from RE lessons by parents did not miss out on a moral education, and that non-religious beliefs are given equal weight.
A public consultation into the draft national RE framework ended on Monday.
A date for publication has yet to be set.
A QCA spokeswoman said: "The consultation was open to everyone, and everyone's views were welcome and will be taken into account. Nothing is set in stone as yet."
According to the QCA, the aim of the framework is to boost public confidence in schools' REwork.