The government is to consider again how best to guarantee seasonal flu vaccines for those at risk after stocks run low.
The vaccine does not protect against bird flu
It blames the shortage on demand outstripping supply, most likely fuelled by public concerns about the threat of a possible bird flu pandemic.
But Health Secretary Patricia Hewitt said GPs may have been giving the vaccine to the worried well rather than those most at risk as recommended.
She said she would review the ordering situation as a matter of urgency.
In the meantime, the Department of Health is advising GPs in England to use remaining stocks only on those at highest risk.
They include the over-65s and people with health problems such as heart disease, asthma and diabetes.
The vaccine does not protect against avian flu, but offers some protection against common winter influenza.
A government expert said GPs either did not order enough vaccines, or have been giving them to people not in high risk groups. That accusation has been hotly denied by doctors.
Those at high risk of seasonal flu have been urged to get themselves vaccinated.
The Department of Health said the 14.5 million vaccine doses that had been ordered by GPs from manufacturers have all been used, which, in theory, should be enough to protect the 11 million people deemed high risk.
The 400,000 doses held by the DoH as a contingency have also been virtually used up.
The DoH said it had ordered another 200,000 doses to arrive by the end of January, but this may be too late for some.
HIGH RISK GROUPS
People aged 65 and older
People with diabetes, chronic respiratory conditions such as asthma, serious heart or kidney disease
People with lowered immunity due to disease or treatment such as steroid medication or cancer therapy
GPs may also decide to give the vaccine to people with serious liver conditions, those living in residential homes and carers of the elderly and disabled
The government has a national target of 70% uptake of immunisation for people aged 65 years and over.
It is not yet known whether all of the high risk groups eligible for the flu vaccine have already had their jab.
This year, for the first time, the government said people who are the primary carers for elderly or disabled patients would be eligible for the vaccine.
The Department of Health said it has now written to GPs in England to inform them that they should no longer order flu vaccine stocks direct from suppliers.
Patricia Hewitt said: "In previous years the GP-led arragement has, on the whole, worked well. In view of what has happened this year, however, I am reviewing the arragements."
Dr Salisbury, head of immunisation at the Department of Health, advised GPs: "Use what vaccine you have wisely and use it for people with high risk factors who should be your priority.
"Those are people over the age of 65 and people under 65 with medical conditions that put them at risk."
He advised anyone eligible for the vaccine who had not yet been immunised: "If you are somebody with a risk factor you should be on your GP's list. Make sure they don't forget you."
Dr Salisbury said there was no evidence that there had been an increased take up among people in vulnerable groups.
"Either GPs did not order enough for all of the people with risk factors, or the vaccine has gone somewhere else," he said.
Flu is estimated to kill several thousand people in the UK each year
10-15% of the population develop flu each year
100,000 flu particles can be projected into the air with just one sneeze
In 12 hours, the flu virus can invade 1 million nose and throat cells
Dr Laurence Buckman, deputy chairman of the British Medical Association's GPs Committee, said: "Patients will feel they have been let down.
"GPs were told there would be enough vaccine and now it seems this is not the case. There is no evidence that family doctors have been using the flu vaccine inappropriately.
"While some practices have had sufficient vaccine, others will currently have to turn eligible patients away. This is unacceptable."
Dr Buckman argued there was little evidence that the vaccine had been given out to those not in the higher risk groups.
He said the current situation showed that previous years' flu vaccine uptake figures were not a good enough measure of what uptake would be in future years.
The chairman of the Royal College of GPs, Dr Mayur Lakhani, said: "I am sure that, by and large, all flu vaccines are being given only to high-risk patients.
"As a College we agree with a targeted approach to flu immunisation."
Last year there was a short delay in the flu jab supply to some doctors' surgeries following a temporary suspension of a manufacturers' licence.
Shadow Health Secretary Andrew Lansley accused the government of trying to shift the blame to GPs.
"The reality is that the government ordered a similar amount of vaccine this year as last year.
"They failed to factor in the threat of avian flu and the new groups eligible for immunisation," he said.
Steve Webb of the Liberal Democrat said: the government's response was simply "not good enough".
"Promising extra supplies in January will leave frail elderly people at risk over the next two months. Winter flu kills over 10,000 people a year. Gaps in coverage among vulnerable groups could be a matter of life or death."