There is a shortage this year of the flu vaccine, which is being described as the "last thing that's needed" in the midst of the Covid-19 pandemic.
A letter being delivered this week to GPs and pharmacies across the country confirms "delays to the deliveries of flu vaccine into Ireland".
The delays and shortages arise even though the HSE is telling GPs and pharmacists it is "particularly important" this year to maximise vaccine uptake among at-risk groups and frontline health care staff so the heath system is not overwhelmed.
"Influenza vaccine is being delivered in a number of shipments, and reduced quantities are being delivered in the initial shipments," the HSE said.
It also admitted rationing "to ensure equitable amounts are available to all sites".
The warning comes as 188 new cases of the virus were announced yesterday, 76 of them in Dublin.
"Encourage your family and friends to heed the public health advice," acting chief medical officer Dr Ronan Glynn said. "Now more than ever, we need to work collectively. Our individual actions count on a population level.
"Every one of us doing our bit in our daily lives - halving our social contacts, working from home, keeping our distance, wearing a face covering, washing our hands - matters a great deal.
"These small, positive steps taken together amount to our best and strongest defence against the virus."
Research carried out on behalf of the Department of Health shows the level of worry among the public stands at 6.5 out of 10.Overload
This is similar to the level expressed in April, with the main sources of concern being health system overload, the health of family and friends and the economy.
Around 47pc think the worst of the pandemic is ahead of us, the highest level reported since April.
Fifty-two per cent think there should be more restrictions, similar to the March figure.
Green Party senator Vincent P Martin said GPs and pharmacists have "grave concerns" for their patients about the initial delivery and roll-out of the flu vaccine.
"Delivery has already been delayed and, worse, the number of vaccines that some doctors have been told they will receive is tiny," he said.
"I have spoken to GPs and pharmacists, one of whom has received 20 vaccines.
"One large GP practice received an initial delivery of 60 vaccines.
"It will not do anything and is nowhere near enough."
GPs and pharmacists are rightly worried and perplexed about this on behalf of their patients, Mr Martin said.
The HSE said it expects to receive a second order by mid-October.