Published Wednesday, 09 December 2009
Health minister Michael McGimpsey said the age group has been identified as the next priority group for the vaccine because they are more likely to be hospitalised if they fall ill with swine flu.
Children under five also have high rates of admission to critical care and there have also been some deaths.
The minister said the decision to vaccinate the age group was supported by advice from the Joint Committee on Vaccination and Immunisation - the UK's independent advisory board on vaccines.
But the government failed to agree a national deal through GP practices.
The row erupted after the government ruled out offering doctors more money.
The government said it had offered doctors £5.25 per dose, plus a "small concession" for GPs to deliver the shots.
The British Medical Association denied it had been pushing for more money and accused the government of refusing to relax targets on how many patients local practices had to deal with.
"I am disappointed we have not been able to reach a national deal with GPs to vaccinate children under five", Mr McGimpsey admitted.
He said he asked the Health and Social Care Board to put in place arrangements for delivery of the vaccination programme.
"I am confident that the vaccination programme will proceed smoothly and know that many Northern Ireland GPs will want to provide this service for their youngest patients", he added.
Children under five will be invited for vaccination before Christmas and the programme will continue into January.
The Health Department said parents will receive information about swine flu vaccinations as soon as the plans have been finalised.