Some pharmacies cannot meet the demands for the nasal flu vaccine, while others have surplus doses.
According to the Irish Pharmacy Union (IPU), 450,000 doses of the nasal vaccine have been distributed but just a quarter have been administered.
The HSE says it is not aware of any supply issues regarding the nasal flu vaccine, with Dr Siobhán Ní Bhrianin adding that the flu vaccine is also available through GPs if people have difficultly accessing it through their pharmacy.
The vaccine is free for children aged between two and 12-years-old and the current batch is due to expire in January.
General Secretary of the IPU, Darragh O'Loughlin says surplus doses from some pharmacies should be redistributed to areas with a higher demand.
"We have been in touch repeatedly with the HSE to tell them that there are areas and particular pharmacies that can't get as many vaccines as they need to meet the demand that they have.
"With the nasal one, if there's a mismatch between supply and demand, communication in and out of the HSE just needs to be improved, so we can get those vaccines to where people want them."