NHS England insisted the issue should be resolved by this weekend and assured patients there is a sufficient supply for the winter.
The vaccination is available every year on the NHS to help protect adults and children at risk of flu – as well as its complications.
Anyone aged 65 or over is advised to get the vaccination by early December.
But delivery delays of the vaccine from manufacturer Seqirus has meant some older patients been unable to get vaccinated.
Doctors’ leaders said the delays for early vaccines were due to them being delivered in a “phased approach” which was meant to ensure the supplier could manufacture them safely and regularly.
A survey of 650 GPs in Pulse found that 68.5% said their practice suffered a shortage of adjuvanted trivalent flu vaccine (aTIV).
Only 20% said they had not had trouble securing the vaccine.
The GPs surveyed said the shortage meant they were unable to vaccinate as many elderly patients as they would have liked.
Seqirus is only delivering the aTIV vaccine in a phased process, with 40% delivered in September, 20% in October and 40% in November.
Practices had been told by NHS England that all flu vaccines would be delivered by 17 November 2018.
Dr Richard Vautrey, GP committee chairman at the British Medical Association (BMA), said NHS England “must learn lessons from the disruption seen in the past weeks”.
He said: “Adequate notice and guidance to all practices must be given well in advance of the ordering period, to allow both practices and manufacturers to ensure there are no further supply problems for next year. Improving information for the public would also be beneficial.”
An NHS England spokesperson told Sky News: “This survey of little more than 1% of GPs ignores the fact that this week, 100% of vaccines will have been delivered by the manufacturer to those surgeries and pharmacists who placed an order on time.
“The public can be assured that – as the BMA has confirmed – there is sufficient supply of the vaccine in stock for everyone to get protected ahead of winter.”
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