GPs might have to relinquish control of ordering future flu vaccines after complaint's about this winter's programme, according to the Government's director of immunisation.
Professor David Salisbury said there are issues over the way GPs are paid for the task but there is a "pretty compelling" case for the Government to take control.
Shortages of this year's seasonal vaccine have had to be bolstered by the Government releasing stocks from last year's swine flu jab.
Ministers acknowledged that there had been geographical "mismatch" with some areas suffering a limited supply and others having too much vaccine.
Reports have emerged of some GP surgeries having to turn away angry patients as doctors ran out of the jabs.
Despite the shortages, GPs remain adamant that they did not under-order stocks of the vaccine.
They base their annual orders for the seasonal flu treatment on the requirements of previous years.
Prof Salisbury's comments come just a day after the Government published draft legislation which would see 80% of the NHS budget pass to GPs with control of commissioning services.
In an interview with the BBC, Prof Salisbury, who is reviewing the current vaccine ordering and supply programme, said GPs purchasing the jab was a "sort of historic hangover" based on their knowledge of how many people fall into at-risk groups.
But new information systems meant this could be monitored in other ways.
He said: "Given where we are now with the degree of intimacy between ordering and supply we need to question whether that could be done differently.
"The question is: can we find a more effective way of contracting and purchasing and then monitoring and distributing using the sophistication that we now can bring to the process?
"Some of the reasons why we didn't do it before are no longer as robust because of the sophistication of the information systems that we now work with."
Richard Vautrey, deputy chairman of the British Medical Association's GP committee, told BBC Radio 4's Today programme: "We would need a lot of convincing that this scheme would improve things.
"It does seem very puzzling. We are being told we are going to get huge responsibilities to run services locally and yet ... the seasonal flu campaign, for some reason there's a suggestion that we change a system that works well."
Copyright © Press Association 2011
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Yes for a small minority but if patients attended when invited there would not be a problem. This is just media hype but also proves to me that those at the top are out of touch with the grass roots of medical care.
John Young, Devon
I dont think we under ordered. A week before Christmas, we had around 30 vaccines left. This would be normal at that time of year. The issue was
that the press whipped up interest in that and the following four weeks which was necessary due to the outbreak of swine flu. These outbreaks will
always be impossible to judge so who is to say that this would be any better managed centrally, in fact, I suspect it would be worse. We shared the vaccine we had in Herefordshire as best we could. There was plenty of swine flu vaccine available at that time anyway so no one went without vaccine here. We have since managed to source more normal flu vaccine and have vaccinated all patients who have needed it.
Julie Burgess, Hereford