Bedfordshire and Hertfordshire LMC said some practices continued to use Meningitec for the single MenC priming dose in three-month-olds despite a change in the schedule last year saying practices should use other vaccines.
The LMC, which said the incident was 'serious' but posed a low risk to infants, warned practices to review how they receive and act on changes to vaccine schedules.
Public health officials announced in May 2013 that Meningitec should not be used as a single priming dose in infants because this did not provide adequate protection against meningococcal C disease.
Practices were expected to use only Menjugate Kit or NeisVac-C vaccines in this age group from June 2013.
Public Health England (PHE) contacted all practices that continued to order Meningitec after the schedule change and asked them to report back on action taken, but only half of 61 local practices responded, the LMC said.
A subsequent investigation found 30% of local practices had no systems to act on changes to vaccine schedules, and half of these practices had no arrangements in place to respond to serious incident investigation.
In a newsletter to local GPs, the LMC warned practices that although the risk to infants was low in this case, it was a 'serious incident' and practices were expected to follow advice on schedule changes.
The LMC said: 'We understand that the volume of emails you receive means that it can be easy to overlook something so important, but it is vital that practices have systems to respond to alerts sent out by the area team.'
GPs have faced a series of changes to vaccination schedules over the past year, including programmes for shingles, rotavirus, flu, MMR and meningitis C vaccinations.
Dr Mary Ramsay, head of immunisation at PHE, said: 'When a vaccine schedule is changed there may be some teething problems with implementation and ensuring the correct doses are given on time.
'Currently, meningitis C disease is extremely rare in the UK, especially in children. The risk of meningitis C disease in any infant, including those who may have only received a single dose of Meningitec is, therefore, likely to be very low and for a very short period.
'Parents should be reassured that their child should respond well to the 12-month booster dose whatever MenC vaccine they received at three months of age. All children should receive the 12-month booster on time but this is especially important for children who have only received a single dose of Meningitec.'
PHE said NHS England area teams had alerted practices where this error may have occurred and asked them to contact parents. By the end of the year, all infants who had received the Meningitec vaccine at three months in error should have been given the 12-month booster dose.