The BBC has been forced to apologise to an acclaimed psychologist and writer after editing her derogatory comments about religion so that a radio programme broadcast "the opposite" of what she had said.

Dorothy Rowe complained to the corporation that her interview on the Radio 2 programme What Do You Believe? had been so heavily edited that the final version misrepresented her views. During a 50-minute recorded interview, Rowe, best known for her work on depression, had attempted to comment on the subject proposed by the programme's producer: "Why so many people want to believe in God and search for faith." But she was aghast to hear how her words were eventually used.

In an email to the corporation, published on her website, Rowe stated: "My words were edited to make it sound that I held a favourable opinion of religion in that it gave a structure to a person's life. What was not broadcast was what I had said about how such structures can be damaging to people. Being misquoted in this way concerned me greatly."

Rowe, who says she is one of the BBC's biggest fans, was never likely to keep her complaints private. An Australian who spends much of her time in the UK, she has become one of the most respected modern-day thinkers, named as one of the six wisest people in the UK by a magazine and voted one of the world's 100 living geniuses in a global poll.

Rowe, who is in Australia promoting a new book, said on her website she had no option but to complain as she was acutely aware of the dangers of "having something in the public domain that did not represent my views" and which would "could cause me considerable problems, particularly when the subject matter was religion". She said the interview "sounds like I am giving unqualified praise to religious belief. There is no mention of what I talked... about at length, that religious belief can cause immense misery. I often summarise this with: 'The church keeps me in business'."

The latest row over the BBC's production methods comes soon after the Jonathan Ross and Russell Brand saga and a string of phone voting scandals which have undermined confidence in the corporation. The BBC has promised to introduce tighter editorial controls.

After hearing the broadcast, Rowe emailed David Barber, the BBC's head of compliance. Barber, who later resigned over the Ross-Brand furore, passed the complaint to Christine Morgan, executive producer at the BBC's religion and ethics department, who apologised to Rowe, saying she was "very concerned to find that, as you say, the programme did not accurately reflect the view you expressed". But on her website Rowe accuses Morgan of "saying she was sorry I was distressed, not that she was sorry that I had suffered an injury".

The row has provided ammunition for secular critics who accuse the BBC of using its programmes to promote religion. Terry Sanderson, president of the National Secular Society, who was interviewed for the same programme as Rowe, said: "I gave a long interview, but when I listened to the finished product it contained just a couple of very brief soundbites from me which were not representative of the thoughts I had expressed... This programme was the most blatant piece of religious propaganda I have heard for a long time."

A reply to a Freedom of Information request passed to the Observer reveals that the corporation spent almost £10m last year on its religious affairs unit in Manchester. According to the BBC's annual report, religious broadcasting on BBC radio rose from 1,078 hours in 2006-07 to 1,114 hours in 2007-08.

A spokeswoman for the corporation said: "The BBC's religion and ethics department acknowledged that extracts from an interview with Dorothy Rowe - broadcast in the programme What Do You Believe? - misrepresented her views on religion and has apologised to her."

Rowe was also invited to write an article published on the BBC's religion and ethics website explaining her views.