GPs demanded the right to charge private fees for treatment not funded by the NHS in a motion passed at the LMCs conference in May.
Delegates also heard calls that this should allow ineligible patients to obtain the flu jab from their GP.
But GPC deputy chairman Dr Richard Vautrey said this could see GPs taking the flak for supply woes. 'This would be difficult as we would want to avoid the situation where flu vaccines become unavailable to patients who really need them,' he said.
'It is not unusual for vaccine shortages to arise and we would not want GPs to be blamed for causing this by giving flu injections to those who are not at risk before the patients who are at risk have been vaccinated.'
At the LMCs conference, Dr Jag Kaliray of Leicestershire and Rutland LMC said 'clear demand' among patients who are ineligible for the vaccine on the NHS was currently met by private providers, such as pharmacies.
'Patients trust us and would wish to be vaccinated in surgery. It is fair that they should be able to have these vaccinations in surgeries if they wish.'