Northern Ireland is almost 200,000 doses short of the flu vaccine and at this stage cannot complete its vaccination programme.
Dr Alan Stout, chair of NI’s GP committee (NIGPC) said he was “deeply concerned and frustrated about the shortfall”.
The Public Health Agency (PHA) said it acknowledged the “inconvenience”.
The shortage emerged at a meeting of GPs and Public Health Agency representatives, said Dr Stout.
“The shortage affects the over 65 age group.
“We cannot deliver the flu programme until we actually see the vaccine in fridges.”
The PHA said the demand for flu vaccine this year had been “phenomenal”.
“This demand has resulted in a temporary pause in the supply of vaccine for eligible people under 65, and additional controls to ensure fairer distribution to all GP practices across Northern Ireland,” a spokesperson said.
“To date we have distributed more vaccines in the past few weeks than the entirety of previous flu seasons.”
Dr Stout said there was “no point” booking clinics and arranging for people to turn up “until we physically have it in our hands”.
GP practices have been advised not to book any further vaccination clinics.
In correspondence to GPs across Northern Ireland seen by BBC News NI, Dr Alan Stout wrote: “You can probably sense my frustration.”
An additional 200,000 doses have been ordered but no date has been confirmed for when they will arrive.
The PHA advised GPs the order may come “next week, by the end of the month but they did not know for sure”.
The NIGPC has written to the Chief Medical Officer (CMO) Dr Michael McBride voicing their concerns.
Northern Ireland did not receive its full vaccine quota – while one million doses were ordered, between 500,000 and 600,00 were delivered.
There are two different flu vaccines available for those over 65 and a different one for those below 65.
Another problem, according to Dr Stout, is they do not know exactly how many over 65s still have to be vaccinated.
“We need to see the actual vaccine in fridges, we need the support in place and we need to have the approval to give the vaccine that we have for those below 65 to those who need it who are above 65,” he said.
“We cannot do that without advice from the CMO.”
Dr Gerry Waldron, head of health protection at the PHA, said he regretted some flu clinics had to be cancelled.
However he added: “I would like to provide reassurance that people will still get the vaccine well in time before we anticipate that flu will be circulating widely in the community.”
At a meeting last Wednesday, PHA officials asked GPs for ideas about how else the vaccine could be delivered or what help could be provided.
It was also confirmed that the chief medical officer would be asked to give his permission so that GPs could administer the under-65 stock instead.
This could create potential problems for the roll out of the Covid-19 vaccine, according to Dr Stout.
“There needs to be at least three weeks between receiving the flu vaccine and the Covid-19 vaccine,” he said.
“While there is no date for the latter yet and no correspondence at all about how NI will administer that – we want to made sure as GPs that the flu vaccination programme is complete.”