Chaplaincy care has been reduced by 54,127 hours a year since 2005, the findings of a survey by Theos showed.
It questioned 198 NHS trusts in England, and found almost a quarter had made "major cuts".
The Department of Health said it was down to NHS trusts to make decisions on chaplaincy to meet local needs.
Range of faiths
Currently there are about 400 full-time chaplains and 3,000 part-time chaplains in NHS Trusts in the UK.
They are provided by churches, but paid for by health trusts.
The choice for NHS Trusts should not be between the clinical or pastoral needs of patients said
Paul Wooley, director of Theos.
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 also help staff and relatives cope with death and serious illness.
Paul Wooley, the director of Theos, said doctors and nurses are not able to cover the role chaplains provide.
"The pressures that are on them as medical staff simply don't allow for that," he said.
"Particularly when a patient has died, there's a sense where the medical staff have to move on to the next patient but the chaplain is there to support the relatives who are going through the trauma of bereavement."
Highest loss
Theos' survey found where trusts had made cuts, the average reduction was 19 hours a week.
The highest loss was at Epsom and St Helier University Hospitals NHS Trust, where 22 sessions a week - 77 hours - were lost, or more than 50% of the trust's healthcare chaplaincy, according to the report.
This was followed by North Bristol and Oxford Radcliffe, where 14 and 11 sessions have been lost respectively.
Only two trusts, Lincolnshire Partnership and County Durham and Darlington, reported an increase in the number of chaplaincy sessions available.
Mr Wooley added: "The choice for NHS Trusts should not be between the clinical or pastoral needs of patients.
"Trusts are clearly under serious financial pressure, but if they are to provide holistic care the provision of appropriate chaplaincy support must be a priority."
Spiritual care
A Department of Health spokeswoman said: "We are committed to the principle of ensuring that patients and staff in the NHS have access to the spiritual care that they want, whatever faith or belief system they follow.
"Budgetary control has been devolved to the local NHS to allow people on the frontline to make the decisions about how best to use the resources available locally.
"Local NHS trusts are responsible for delivering religious and spiritual care in a way that meets the diverse needs of their patients, including NHS chaplaincy services."
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