A Monaghan-based GP says the vaccine distribution system is not working, and questions have to be asked.
It comes after the Health Service Executive (HSE) has stopped the distribution of the flu vaccine, after claims emerged that 600,000 doses have apparently gone missing.
A letter was sent to doctors and pharmacists saying only 700,000 of the 1.3 million jabs have been administered, according to the Irish Independent.
The HSE has rejected those claims and said some 50,000 doses were held back to ensure they would be delivered to areas most in need.
The flu vaccine has been in extremely high demand this year because of the coronavirus pandemic.
Healthcare workers have been told to prioritise the vulnerable with any remaining stock.
But Dr Ilona Duffy told Pat Kenny there are a number of questions that need to be answered.
"We became aware that we were limited in how many we were able to get - and we were advised again that was because of a slowness in the vaccines arriving to the country, but that that would be sorted and we'd start to see them.
"But the vaccine deliveries continued on a fortnightly basis and around the country GPs have been complaining - and our pharmacy colleagues as well - that they just couldn't access enough vaccines.
"So to get a letter like this yesterday - telling us that 1.3 million vaccines have been delivered - seems extraordinary that the HSE don't know where these vaccines are.
"We know that they obviously have a record of where they've been delivered to".
'240 vaccines for 11,000 patients'
"The big question is where are the vaccines - I know the HSE are coming out very strongly today and saying the vaccines aren't missing, they've been delivered and they're blaming a delay on claiming them.
"So they're now trying to say 'these vaccines have been delivered, we just aren't sure that they've been administered' - so why aren't they sure?"
"The HSE are now saying these vaccines aren't missing - but I would still ask the question: if they say to me 'We've delivered 100 vaccines to Illona Duffy and she's only claimed for 30', why isn't somebody picking up the phone and saying 'What's happened to the other 70 vaccines - have you delivered them or is it just a slowness in claiming for them'".
"But I can categorically say as a GP in a practice of 11,000 patients, we've received 240 of the flu vaccines.
"So there's something wrong with the whole process, it's not working, and again questions have to be asked and answers have to be sought".
Dr Duffy has concerns the roll-out of any potential coronavirus vaccine could be hit in the same way.
"I'm not confident, given the way that the roll-out is here.
"GPs and our pharmacy colleagues every year manage the flu vaccine programme really well, but this year because of the delays and because of the difficulties in accessing the vaccine".
"And remember these are people who are at-risk, who have been told to get the vaccine and now are being told that they won't be able to get it.
"And I think the message needs to come out that this isn't the GPs fault and it's not the pharmacy's fault: it's because they cannot access the vaccines through the HSE system".