The Department of Health and the Health Service Executive had planned to add two new vaccines to be given by GPs, to all babies born after 1st October.
The planned expansion of the current vaccination scheme was due to come into effect from 1 December.
These vaccines protect against conditions such as meningitis, septicaemia and serious cases of diarrhea.
However, GPS in the Irish Medical Organisation have warned of delays to the rollout of the vaccines.
The organisation said it had a meeting with the HSE six weeks ago during which it said extra resources and fees would be required to go towards the additional GP and nurse time required to extend the vaccination scheme.
However, GPs say they have not had any contact from the HSE about the matter since.
In a statement, the HSE said there would be a timely rollout of the programme once the matter of a fee for GPs has been resolved.
Dr Austin Byrne of the IMO's GP Committee said the vaccines are important and GPs have played a "key role in ensuring that Ireland has one of the most effective immunisation regimes in the world but this experience makes me fearful that this will be lost."
He said the delay is due to a lack of engagement between the HSE and the department and the IMO and the administering of the vaccines will mean that visits to the GP will be twice as long and GPs must be reimbursed for this.
Speaking on RTÉ's Morning Ireland, Dr Byrne said: "There are no additional visits but the visits that will take place at two months, four months and six months will be significantly longer and the HSE's own advice on this is that we need to apply an allocation of about twice the amount of time - so twice the amount of nurse time or twice the amount of GP time."
He said that there are 65,000 children who are due to receive these vaccines.