The additional funding will come from the DoH budget and will help surgeries to contact patients, administer the vaccine and if necessary take on extra staff.
The GPC has also agreed that no changes will be made to the quality framework for 2010/11 to allow GPs to focus fully on swine flu.
GPs who hit the uptake levels of the swine flu programme, still to be decided by the DoH, will see the thresholds for achievement of QOF indicators on patient experience lowered, and the collection data for data on childhood immunisations will be delayed by six weeks to mid February to allow practices time to carry out the swine flu vaccination programme.
Local enhanced services (LES) funding will not be withdrawn to fund the vaccination programme.
It is currently expected that patients will receive two doses of the vaccine, although Dr Peter Holden, GPC lead for pandemic flu, told Healthcare Republic that it was likely that latest research showing that one jab is effective would be looked at by the European Medicines Agency (EMEA).
Health secretary Andy Burnham said: ‘I am glad that we have reached a fair deal with the GPC and I am pleased that GPs will continue to play a key role in the fight against swine flu.'
GPC chairman Dr Laurence Buckman, added: ‘We are pleased we have reached a national agreement as we believe this is the best way to deliver the vaccine to the at risk population.
‘This will be a lot of additional work for practices, but general practice is used to running large vaccination programmes.'