pharmacies may be deterred from giving flu jabs because the €15 fee they are to be paid by the HSE is too low.
The Irish Pharmacy Union fears the take-up level will be lower than expected because pharmacists will decide it is not worth their while.
GPs are getting around ¤42 to administer the vaccine, but this is due to be reviewed.
Darragh O'Loughlin, from the Irish Pharmacy Union, said: "It was a policy decision that we wanted to be able to administer flu vaccines because it's something pharmacies do in the US, Portugal, and the UK.
"We understand that the fee is low and we're disappointed that it's so low, because it might deter pharmacies from providing the service.
"The idea is that fewer people get the flu and end up with secondary infections in emergency departments, so it makes a saving for the State.
"I can't explain why it is that we're being paid a fee that is almost two thirds lower, only the minister can explain that. Currently GPs get around €42."
The difference between the two fees has not been settled yet, and the Irish Medical Organisation is awaiting the minister's decision on the reduction in the GPs' fee.