Practices in some areas have been forced to cancel flu clinics until next month as they try to find other supplies.
The college said the DH should release emergency vaccine supplies to protect patients against flu as problems with deliveries from one leading manufacturer continue.
RCGP immunisation lead Dr George Kassianos said: 'Unless we supply these practices with vaccine now, we shall see a reduction in uptake in those practices. This should not be allowed to happen and the DH has a responsibility here to mobilise its emergency supplies to allow practices to carry out the flu vaccinations.'
A DH spokesman said: ‘We are rescheduling our own deliveries for our strategic reserve to give GPs priority. This will mean there is more vaccine available for them.’
Manufacturer Crucell voluntarily suspended deliveries of vaccines Inflexal V, Isiflu V and Viroflu more than two weeks ago. It supplies 10% of the UK's seasonal flu vaccines.
Deliveries continue to be held back as two batches are investigated on patient safety grounds, the company said.
Speaking at a GPC press briefing this week, GPC chairman Dr Laurence Buckman said: ‘We are aware that there are some parts of the country without access to flu vaccines.
‘We have heard the complaints of GPs who have said, "We can’t get any vaccine for our patients, what is to be done?" The government says that this is a problem they will find ways of dealing with but we are not aware of what they are. Certainly, we don’t have solutions to that at the moment.’
Tracy Green, practice manager of Hartland Surgery in North Devon, told GP her practice had received only one third of the vaccines it needed for this winter. 'We are cancelling around 150 appointments, luckily not more as we stopped booking when we knew of the problem.'
She said the surgery would have to wait until the end of November to receive half of the remaining doses required.
Dr Kassianos said it was vital practices use more than one supplier when ordering flu vaccines. 'I have heard of practices that have not given a single flu jab yet as they placed their flu vaccine orders with the one manufacturer that has delivery problems this year. It is of paramount importance that we order our vaccines from three, or at least two, manufacturers.'
A Crucell spokeswoman said: ‘Customer safety is our top priority and therefore we are waiting until we have final results on the quality of these two lots before releasing any of the vaccines in the 2012/13 flu campaign.’
Dr Maureen Baker, RCGP health protection lead, said: 'We have spoken to colleagues in the DH in England and it is our understanding that other companies have managed to bring in more stock to cover the Crucell shortfall.
'Affected practices should therefore contact those companies to ensure their supplies.'
- Practices with continuing problems after trying other suppliers can contact the RCGP on email@example.com for assistance.