However, the GPC was not consulted about the proposed changes and virology experts have questioned the new schedule's evidence base.
The changes mean that children will be given the pneumococcal vaccine from some point in 2006/7 and that the scheduling of the Hib and meningitis C vaccines will also change.
CMO Liam Donaldson said giving the pneumococcal vaccine to children at two, four and 13 months would save lives.
'We have already seen the immense impact this programme has had in the US. Since its introduction, cases in young children caused by the strains in the vaccine have fallen by 94 per cent,' he said.
The schedule for the meningitis C and Hib vaccines will be changed to add a booster at 12 months on the back of evidence showing that their effectiveness wanes after a year.
This evidence was cited by the Joint Committee on Vaccination and Immunisation in its advice to the DoH.
However, Dr Nigel Higson, a Brighton GP with an interest in virology, said that not all of the evidence supported the changes to the schedule.
'Giving a meningococcal vaccine alongside Hib results in lower immune protection than if they are given separately,' he said.
'I would give a second dose of meningitis C at five months instead to avoid this. It would also make things easier for GPs by avoiding having to give three jabs at once. It's hard enough giving a child a second injection in the leg, but a third is a danger to patient and doctor.'
Dr Peter Fellows, chairman of the GPC prescribing subcommittee, said that the changes were not negotiated with the GPC and the first he heard of them through media reports.
'We haven't been given the chance to discuss this in GPC so we can negotiate the changes properly,' he said.
Following the announcement in its White Paper that immunisation funds would be split with other providers, the DoH said that NHS Employers and the GMC immunisation subcommittee would negotiate changes to payments in the next phase of the GMS contract review.
The subcommittee is expected to meet with NHS Employers three or four times this year, with changes to the fund-ing arrangements implemented from 2007.
Dr Fellows said he looked forward to the GPC at last being allowed to contribute.
'Like most plans included in the White Paper, these seem to have been written before any consultation,' he said. 'They would make it difficult to properly coordinate vaccinations.'
- Two months: DTaP/IPV/Hib and pneumococcal.
- Three months: DTaP/IPV/Hib and MenC.
- Four months: DTaP/IPV/Hib, MenC and pneumococcal.
- 12 Months: Hib/MenC.
- 13 Months: MMR and pneumococcal.