In a letter to all GPs, Dr Laurence Buckman, chairman of the GPC, said it had not been possible to reach an agreement with the UK governments on a national framework.
Instead, plans should be put in place locally to ensure all eligible children are vaccinated as quickly as practically possible.
Dr Buckman said: ‘We sincerely wanted to be able to reach a national agreement with the UK governments about a process for vaccinating the under fives against swine flu.
‘Unfortunately this has not been possible, because the government would not support adequate measures to help free up staff time. At the busiest time of the year for general practice, with surgeries already dealing with the additional work of vaccinating the first wave of at-risk groups, we felt this was vital in order to ensure this next phase could be carried out quickly.
‘We would encourage LMCs and primary care organisations (PCOs) to put in place arrangements that are sensitive to the workload pressures in their area. These should be agreed as soon as possible.'
Health secretary Andy Burnham said: ‘It is disappointing that we have not been able to come to a national agreement with GPs to vaccinate children from six months to five years old. But we are now getting on with the job and asking local health trusts to put local plans in place so that vaccination of these children can begin seamlessly.
‘The supply of vaccine is increasing and we should therefore be able to meet the demand for vaccine and begin vaccinating children before Christmas.'