The elderly and those with chronic conditions may be put at risk due to delays in delivering flu jabs, GPs say.
The vaccine is given to over 65s and those with chronic conditions
The government has warned doctors some vaccines may not arrive until December due to a production problem and the need to give the most needy jabs first.
The over 65s and people with conditions such as heart disease and diabetes normally get the jab in the autumn.
It is the third year running there have been problems but the government said it was better than first expected.
The Department of Health said there should be enough doses in the long-term but some patients would have to wait and that some surgeries in England would have to share stocks.
The same shortage applies to Scotland, Wales and Northern Ireland.
But the warning coincides with the start of a national advertising campaign reminding people at risk to get their flu jab.
In the past two years, supplies have run short because of excess demand. It was particularly acute last year - possibly because of fears over bird flu - and meant some at risk groups did not receive their jabs until after Christmas.
Cold weather can kill up to 20,000 people a year - a figure which can double in particularly bad winters.
A new flu vaccine has to be produced each year because the virus constantly mutates.
This year there was a problem growing one of the strains which makes up the vaccine, meaning suppliers could not get the vaccine out as quickly as normal.
However, the government has ordered 15.2m doses of the vaccine - a million more than last year when supplies ran out possibly because demand was fuelled by fears over bird flu.
In June, the UK Vaccine Industry Group warned there may be European-wide delays and even shortages due to difficulties growing one of the strains.
Dr David Salisbury, head of immunisation at the Department of Health, said at one point it was even thought the production problems could lead to a shortage of vaccines.
At risk groups
Those aged 65 and over
Those with a chronic respiratory disease like asthma
Those with chronic heart disease
Those with chronic renal disease
Those with chronic liver disease
Those with diabetes
Those with a compromised immune system and those living in long-stay residential care homes or long-stay facilities
"While the overall national picture is more positive than we had first thought, the initial delay in production means that delivery of vaccine will be spread over a longer period," he said.
Dr Salisbury said in future it be necessary to look at new ways to make the vaccine available. At present, 97% of UK supplies go to the NHS, with a small proportion available through retail outlets.
Paul Rayner, chairman of the UK Vaccine Industry Group, said: "While most surgeries have already received details of their revised delivery schedules, the group advises any surgeries who have not yet received this information to contact their supplier as soon as possible to confirm arrangements."
But Dr Hamish Meldrum, chairman of the British Medical Association's GPs committee, warned that the vulnerable could be put at risk by the delay.
"Obviously, the at-risk period for flu outbreaks tends to run from November to March or even April, so even not getting an immunisation until the New Year will still help.
"You're really in the lap of the gods as to whether there might be a flu outbreak in your area before that."
It takes about two weeks after vaccination for antibodies to develop in the body and provide protection against flu.
However, Dr Meldrum advised patients to wait until they heard from their GP practice, rather than phoning for updates.
Shadow health secretary Andrew Lansley added: "I asked ministers two weeks ago for an update on the supply of flu vaccines for this year, and was assured that 15 million doses would be available. Now we learn that they are not.
"I am writing to Patricia Hewitt asking her to issue guidance to GPs on how to protect their patients if a flu epidemic strikes and we do not have enough vaccines available."
Charities also expressed concern that at-risk groups would not be able to get their jab early.
Dr Lorna Layward, research manager at Help the Aged, said: "If an older person develops flu before they can get their jabs, the consequences could be potentially life-threatening.
"The government needs to act urgently to ensure that the most vulnerable people get their vaccinations early in order to prevent unnecessary deaths."