The GPC said many GPs would immediately fall foul of new GMC rules that discourage the use of unlicensed and off-label prescribing, in favour of licensed treatments.
If the GMC takes action against GPs who are in breach of the guidance, it would 'decimate' the profession and raise the NHS drugs bill, the GPC warned.
But GPs who comply with the new rules could be accused of failing to follow NICE guidelines, some of which advise the use of unlicensed medicines.
GPC prescribing lead Dr Bill Beeby said: 'The implications are significant.'
|GMC prescribing rules|
One senior GP, Dr Anita Sharma, welcomed other parts of the guidance, saying that it would help to promote safer prescribing (see expert view, below).
Previously, doctors were permitted to prescribe an unlicensed drug when it would better serve a patient than a licensed one.
The GMC had planned to relax these rules further, but overturned its decision following legal advice on EU law.
The GMC's new guidance, Good practice in prescribing and managing medicines and devices, comes into force on 25 February. It says doctors can now prescribe unlicensed or off-label drugs only when a licensed alternative is unavailable or inappropriate for a patient.
Dr Beeby said the rules were 'vague' and suggested that cheaper generic medicines should not be used off-licence when a licensed product exists - even when there is strong evidence of efficacy.
He warned: 'I suspect that a large percentage of GPs will fall foul of this guidance and the rest will do so over the next week as they prescribe amitriptyline in chronic pain rather than pregabalin.
'If the GMC does not act, its failure to do so will set a precedent. If it does, the GP workforce could be decimated. Drug budgets will then certainly rise and medicines management might be powerless.'
GMC chief executive Niall Dickson said: 'This new guidance tightens current rules on prescribing and addresses the challenges doctors face in this complex area.'
|Expert view: Why GMC guidance will lead to safer prescribing|
Dr Anita Sharma, GP and clinical director for vascular and medicine management, Oldham CCG
'As a primary care clinician, I welcome the GMC guidance. General practices, through investment, have improved their systems to support safe and effective prescribing and continue to do so.
'Repeat prescribing is a perfect example of this: better monitoring and employing more staff have both played an important part in the improvement.
'There is still a long way to go on this and one of the challenges we face in primary care is to get proper information from the hospital. I sincerely hope the GMC guidance will play an important role in improvement in hospital prescribing on discharged patients.
'GPs know that patients do not always take prescribed medications and the scale of non-adherence is huge. I welcome the inclusion of patient involvement in the GMC document. This, in my view, improves compliance and reduces wastage - all parts of good prescribing.
'This is not always possible in a 10-minute consultation, but I feel very strongly that regular reinforcement helps.'