The HSE has denied there is a shortage of flu vaccines and Pneumovax 23, a vaccine which prevents pneumococcal infections, including pneumonia.
Dr Rita Doyle, a GP and president of the Medical Council of Ireland, tweeted that she heard reports that more Pneumovax 23 will not be available until next year.
Other GPs raised concerns that not everyone who requests the vaccine will be able to receive it, much like the increased demand for the flu vaccine this year, with supplies struggling to meet demand.
The Irish College of General Practitioner's Covid-19 clinical lead, Dr Nuala O’Connor, said her organisation understands from the National Immunisation Office (NIO) that there has been a large increase in GPs ordering the PPV 23 vaccine this year.
"The NIO has asked GPs to target those at highest risk for the vaccine.
"The PPV23 vaccine is recommended for everyone over 65, and those in certain high-risk categories under 65 years of age.
"Due to the high demand GPs have been advised to defer vaccination for patients over 65 who are not in a high risk category."
Dr O'Connor adds that GPs with high-risk patients seeking the vaccine are asked to contact the HSE with specific patient information.
"As a GP myself who has always promoted uptake of vaccines, it is regrettable that when there is demand for a safe effective vaccine that I do not have sufficient supplies to be able to give to patients," she added.
"In my practice we have not run out, but I am aware of colleagues who do not have sufficient supplies."
However, the HSE said that there was sufficient stock of Pneumovax for those in the priority group.
"Since 2005, sufficient quantity of Pneumovax 23 vaccine has been provided to vaccinate all people aged 65+ years and those in eligible risk groups," the HSE said.
"A year’s supply of vaccines has been delivered to GPs since September 2020. There has been no change in the eligible at-risk groups for Pneumovax 23.
"Stock is available for those in eligible risk groups who have not been vaccinated before or are due their booster after five years."
There is also an ongoing issue with the supply of flu vaccines.
Dr Mike Thompson, a GP from Midleton, had to close his drive through flu vaccination clinic after one weekend as it ran out of vaccines.
Speaking to the, Dr Thompson said the supply of flu vaccines was not meeting the "staggering demand".
He said they cannot source vaccines privately, so he believes those who previously got the vaccine but are not eligible under HSE criteria probably will not get it this year.
"The most you could accuse the HSE of was under-estimating demand. They are saying they have enough for the HSE eligible population, but I don't know if they will, I think it will be very close.
"We are already being asked to prioritise over 65s and healthcare workers, instead of people with long-term health conditions and pregnant women.
Dr Thompson said if the HSE had vaccines, they would give them, and there was a global supply chain issue at play.
He added that he believed there was enough pneumococcal vaccines locally.
In relation to flu vaccines, the HSE said: "The HSE has procured approximately 1.4 million doses of Quadrivalent Influenza Vaccine (QIV) for adults and children which is over 20% more influenza than was used last season, as increased uptake was expected in the targeted groups.
"The HSE has also purchased 600,000 doses of Live Attenuated Influenza Vaccine (LAIV) for children aged 2-12 years old.
"A total of 950,000 QIV and over 300,000 LAIV influenza vaccines has been delivered around the country, an increase of 10% compared to the same time last season.
"All stock has been delivered to the National Cold Chain Service."