Doctors are demanding that NHS staff be given a right to discuss spiritual issues with patients as well as being allowed to offer to pray for them.
Medics will tell the British Medical Association conference this week that staff should not be disciplined as long as they handle the issue sensitively.
The doctors said recent cases where health workers had got into trouble were making people fearful.
But atheists said it was wrong to mix religion and health care.
The doctors, who are behind the motion being discussed at the Liverpool conference, are unhappy about the guidance that has been issued.
The General Medical Council code suggests that discussing religion can be part of care provided to patients - as long as the individual's wishes are respected.
But at the start of this year the Department of Health issued guidance warning about proselytising.
It said that discussing religion could be interpreted as an attempt to convert which could be construed as a form of harassment.
It comes as NHS trusts have taken a hard-line in a number of recent cases.
Last year community nurse Caroline Petrie was suspended by North Somerset NHS Trust after offering to pray for a patient, although the 45-year-old was later allowed to return to work.
And only last week a Gloucestershire nurse said she had left her job at a local hospital after being told she could not wear a crucifix - although the hospital said it was because of health and safety rules, not religion.
Cancer specialist Dr Bernadette Birtwhistle, who works in hospitals across Yorkshire and is a member of the Christian Medical Fellowship, said: "I think it is getting to the point where many of us feel we cannot talk to patients about their spiritual or religious needs or ask them about praying.
"Christianity is being seen as something that is unhelpful."
And she added: "Freedom of speech is being curtailed too much and I don't think that is always in the benefit of patients."
However, the Department of Health said it was the responsibility of the NHS Chaplaincy Service to meet the spiritual needs of patients.
A 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.
"Although all staff should be sensitive to religious needs and preferences of patients, the delivery of spiritual care should be provided by the hospital chaplaincy service."
And Terry Sanderson, president of the National Secular Society, agreed it was not the role of doctors and nurses to bring up religion.
"We have to be very careful about how we tread on this issue. If we say it is ok for doctors and nurses to provide spiritual care and pray for patients it can all too quickly get out of hand and we will have staff preaching on the wards.
"The risk is that it makes patients feel uncomfortable. They may feel compelled to say 'yes' thinking their care will suffer. Really, it is an infringement of their privacy.
"I think we should be very clear that patients should have to ask for this, not offered it."
But Joyce Robins, co-director of Patient Concern said: "Most complaints from patients are about being on a conveyor belt of care. They don't rate with staff as real people.
"Offering to say a prayer is a warm and kind thought. Most patients will accept it as such. It is no more offensive than being offered a sleeping pill. You can say thanks but that sort of thing isn't my cup of tea.
"But if Christian doctors see this as an opportunity to promote their faith to people at a time when they are particularly vulnerable, that is totally unacceptable."