Professor Malcolm Lewis, GP Director at the GMC, said the regulator's rule on self-prescribing was "unacceptable" and "irrational".
He claimed there is a need for more "permissible" guidance.
"I think the GMC's rule on self-prescribing ought to say something along the lines of 'GPs should not prescribe for friends or family if it is something that would bring their professionalism into question'," he said, "Prescribing yourself some antibiotics for a chest infection wouldn't do that."
Professor Lewis' comments came in response to comments made by Dr Simon Bradley from Avon LMC at the annual LMC conference in Liverpool on Tuesday (22 May).
Dr Bradley claimed the GMC's "blanket and insensitive approach" to self-prescribing breaches GPs rights "as expert patients".
However, medical defence organisation MDDUS has urged caution.
It has advised GPs to seek an "objective opinion" of a fellow GP and refrain from self-prescribing.
"Self-prescribing is not technically illegal, but the GMC makes it clear that it should be discouraged, stating that doctors should, wherever possible, avoid treating themselves or anyone with whom they have a close personal relationship, and should be registered with a GP outside their family" says MDDUS Medical Adviser Dr Barry Parker.
"Doctors recognise that self-prescribing drugs of dependence such as opiates or powerful painkillers is entirely unacceptable, but the reality is that they should also avoid diagnosing and treating themselves or loved-ones with other medications. If not, they may be called upon to justify why it was necessary to prescribe in these circumstances.''