A growing number of patients attending the Homoeopathic Hospital in Glasgow, the only one of its kind in the country, are now having to pay privately for treatments recommended by their consultant.
Following the closure of the hospital's pharmacy last year, patients now have to get their GP to sanction their prescriptions.
But some doctors are no longer approving the medicine on the NHS amid an increasingly vocal rejection of the benefits of the treatment by the conventional medical profession.
Health Secretary Alex Neil has criticised the GPs' stance, saying they have a "moral duty" to allow their patients the medicine prescribed by the hospital.
Mr Neil told a public meeting in Glasgow this week: "My view is that if a GP is referring a patient to the Homoeopathic Hospital I think they are duty bound and morally bound to be prepared to write a prescription if that is the outcome of these visits. I don't think this is just an issue that affects Glasgow."
Users of the hospital, which is also known as the Centre for Integrative Care, told the meeting they were concerned about the future of the service.
Up to 800 patients are seen there every year but the care on offer has already been cut back, with overnight beds reduced and the hospital no longer running a seven-day-a-week operation.
BMA Scotland has urged NHS Scotland to halt its £1.5 million funding of the hospital until more proof exists about the effectiveness of homeopathy.
GPs can refer patients who are suffering from a number of serious health conditions, from cancer to multiple sclerosis and Crohn's Disease, for treatment that often supplements more conventional medical care. However, patients can choose to be solely treated at the hospital.
As well as homeopathy, which derives it remedies from plants, animals and minerals, the hospital also offers dietary and self- care advice, physiotherapy and reflexology for those living with long-term medical problems.
Robert Calderwood, chief executive of NHS Greater Glasgow and Clyde, said he has met GPs to discuss the issue of homeopathic prescriptions.
Mr Calderwood said: "Our own view is that if a GP makes a referral to the homeopathic hospital that is because he or she thinks the patient will benefit from it and should make the prescription available.
"A number of GPs are refusing to do that and we are sympathetic to the individuals involved."
Mr Calderwood has long maintained the future of the hospital could be in jeopardy if money was not being made available to fund the service for those using it from other parts of the country.
He stressed there were no plans to close it but a "redesign" of services may be required.
NHS Lanarkshire and NHS Lothian are currently deciding whether to continue funding for homeopathy and NHS Highland has already withdrawn its funding for patients.
Dr John Ip , medical secretary of the Glasgow Local Medical Committee, which represents all GPs in the Glasgow area, said GPs were not trained in homeopathic medicine, and most people were not aware of any evidence of its effectiveness.
Dr Sara Eames, president of the Faculty of Homeopathy, said she sympathised with doctors who did not want to prescribe medicines they were unfamiliar with, adding that basic training in homeopathy for GPs could be a solution. She said the hospital could form an arrangement with a local homeopathic pharmacy to cut out the need for patients to go to their GP.