The British Humanist Association called the newly published BBC Impartiality Review "a fatal missed opportunity".
The review sought to assess the range of voices and viewpoints in BBC output in relation to its news, current affairs and factual output, including whether 'due weight' is given to a range of perspectives or opinions, such as whether views held by a minority should given equal weight to the prevailing consensus.
The BBC's coverage of immigration, religion and the EU was analysed by Cardiff University.
Former ITV chief executive Stuart Prebble who led the review for the BBC Trust found their had been "slowness in the past in accommodating changing opinions on immigration and the EU" and an "over reliance" on voices from Westminster.
The BHA criticised the BBC for failing to provide programmes on non-religious beliefs such as humanist ones, which it is obliged to do under the Communications Act 2003.
The broadcaster has said it will create a pan-BBC forum on religion and ethics in the wake of this review.
Atheists have often criticised the BBC for broadcasting programmes like Songs of Praise, and 'Thought For The Day' on BBC Radio 4's Today programme - which only religious commentators and clergy are allowed to deliver.
Pavan Dhaliwal, BHA Head of Public Affairs, said: "Given the massive demographic and cultural shifts occurring in UK society right now, this review is hugely disappointing. It totally fails to engage with the reality of society today - the society the BBC is set up to serve - and to anyone who cares about good quality broadcasting on beliefs and values it represents a fatal missed opportunity.
"The BBC simply cannot expect to continue to command public support if it continues as it is in relation to its religious output, neglecting the beliefs and values of the majority of licence payers.
"It's difficult to think of a report that could have had weaker coverage of the relevant issues or worse recommendations than this."
This week, Channel 4 announced it is to broadcast the Muslim call to prayer every morning during Ramadan - a decision which the broadcaster called a "provocation" to those who only associate the religion with terror and violence.