The society says churches should pay for hospital chaplains
Religious groups should fund their own presence in UK hospitals and save the NHS some £40m per year, the National Secular Society (NSS) suggests.
The organisation of non-believers says such money would be better spent on "much needed" nurses or cleaners.
The NSS claims even organ players in hospital chapels are on NHS payrolls.
NHS guidance notes all patients have a right to religious observance and that trusts should provide both faith representatives and places to pray.
However, the Catholic Church in Scotland said it agreed that spiritual carers should not be funded by the NHS.
'Pressure on services'
The NSS said it contacted 233 acute and mental health trusts which spent a total of £26.72m on chaplains, at an average of £48,953 each.
The society extrapolated these figures for the whole of the UK to produced a national average of £32m.
But the NSS said this took into account only the salaries of the chaplains, and excluded national insurance contributions, pension payments, administration costs, office accommodation, training, and the upkeep of chapels and prayer rooms.
NSS president Terry Sanderson told BBC Radio 4's Today programme that the £40m figure was equivalent to employing 1,300 nurses or 2,645 cleaners.
"I think if people were given the choice they would choose the latter [nurses or cleaners] because frontline services are under pressure, they are going to be increasingly so as the recession bites, and it's important that savings are made wherever they can be," he said.
But Father Paul Mason, a Roman Catholic hospital chaplain in London, said there was a call from patients for chaplaincy services.
"We are all busy, there is a demand, we're not there because we're trying to find something to do, we are there because there is demand on the ground for chaplains to be present," he said.
The Reverend Chris Swift, a former president of the College of Health Care Chaplains, said: "The NSS report is based on erroneous and simplistic assumptions that do not delve into the real work that chaplains from all faiths carry out in the NHS on daily basis in often emotionally fraught situations."
The role of NHS chaplains - who come from a range of faiths and denominations including Anglican, Roman Catholic, Jewish and Muslim - ranges from visiting the sick, to administering sacraments and advising on ethical dilemmas.
They are also expected to help staff and relatives cope with death and serious illness.
But the NNS says these services are part of churches' own "fundamental responsibility", and as such should be paid for out of their own pockets.
"Most people who go into a hospital come from the local area and it would be better if their own vicar, priest, rabbi or imam came to see them if they felt in need of religious support," Mr Sanderson said.
"This could be done as part of the clergypersons' regular duties - it should not fall as a burden on the NHS."
He added that in some cases organists were on the payroll to play in chapels and in other instances Catholic priests delivering last rites charge the hospital a "call-out" fee.
The organisation said it was asking the Department of Health to conduct more thorough research into the extent to which these services were used by patients, and how appreciated they were.
A Department of Health spokesman said it was "committed to the principle of ensuring that NHS patients have access to the spiritual care that they want, whatever faith or belief system they follow".
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The spokesman said: "Chaplains do an extremely demanding job, often in difficult circumstances, and their skill and dedication is highly valued by patients, relatives and staff within the health service."
A Church of England spokesman said: "Spiritual healthcare has long been acknowledged, by both medical practitioners and the churches, to be an intrinsic part of caring for people in hospital.
"NHS Trusts pay for chaplaincies because they see them as part of their duty of care to patients, not because the churches force them to."
But Peter Kearney, a spokesman for the Catholic Church in Scotland, said: "The Catholic Church in Scotland agrees that religious and spiritual carers should not be employed by the NHS nor funded by the NHS.
"Priests will not become employees of Health Boards nor receive any payments for duties which are part of their pastoral ministry."