Drugs intended for UK patients are being exported for sale abroad to take advantage of exchange rates and there have been issues with pharmaceutical company quota systems.
The Chemist and Druggist Stock Survey 2010 found more than 80 per cent of pharmacists think getting hold of branded medicines is tougher than ever, leaving patients facing long waits.
The Parkinson's drug Sinemet, breast cancer drug Femara, schizophrenia medicine Zyprexa and the anti-depressant Cipralexare are among the most difficult to obtain.
Almost 90 per cent of pharmacists spend more than an hour a week trying to source key medicines and most said they were braced for worse to come in 2011, with 60 per cent predicting wide shortages.
Some said shortages have triggered distress and suffering in patients with life-threatening illnesses. More than 40 pharmacists said patients had suffered as a result, ranging from "anxiety and distress" to hospital admissions.
Of the more than 200 pharmacists surveyed, 27 per cent had known a patient whose health had suffered following difficulty sourcing a medicine.
More than seven out of 10 said they were very concerned their patients had been affected.
Some 93 per cent of pharmacists have had to ask a GP to change a prescription because of problems sourcing a drug.
Chemist and Druggist said there had been six months of talks between the Department of Health, manufacturers, pharmacy bodies and wholesalers to solve the crisis.
But 86 per cent of pharmacists said these efforts so far were poor, with some saying more than 50 drugs were still out of stock at their wholesalers.
Manufacturers have blamed parallel trading of UK medicines to the EU as the cause of the shortages.
Drug firm Novartis told Chemist and Druggist: "Differences in medicine prices between the UK and other parts of Europe can lead to a small number of businesses and individuals ordering medicines to re-sell overseas for profit."
The Association of the British Pharmaceutical Industry has called for urgent Government action to stop the overseas sale of medicines intended for UK patients.