The lack of FLU has left thousands of people over 65 who could not get hit.
Patients have been repeatedly turned away by doctors and pharmacies.
And while fresh supplies should be available next week, there are fears that many older people will not bother returning.
Weaknesses have been noted in many areas such as Bristol, Kent, Devon, West Sussex, Essex, Derbyshire, Middlesbrough and Liverpool.
Daily Mail sources reported that the latest vaccine, called Fluad, is more effective, but could not be ordered until later than usual. Some doctors say there has also been a delay in obtaining official advice on how to use them.
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John Kell of the Patients' Association said: "This poses a very worrying risk to patient safety and could put the NHS under further pressure."
NHS data released yesterday indicate that the vaccine currently has 45.2 percent over 65 years of age, compared with 61.9 percent in the same period last year.
NHS England said the strike "will be available to all in time when the flu season usually begins in December."
Bristol, a pharmaceutical physician, John Billing, said he turned away up to 15 patients a day.
He said: "It is getting to the point where some patients say" well, I will not forget it until this year. ""