Ministers have been accused of attempting to cover up their "gross negligence" over the shortage of flu vaccine by blaming GPs for the crisis

Opposition MPs condemned the situation as a shambles as figures from the Department of Health showed millions of doses of flu vaccine were unaccounted for.

The department revealed yesterday that its emergency supply of the vaccine had dwindled to 50,000 doses amid demand from GPs running out of the jabs. Senior Department of Health officials have warned doctors about a shortage of the vaccine and urged them only to give the injections to at-risk patients, not the "worried well".

Patricia Hewitt, the Health Secretary, said she had ordered an urgent review of the vaccination programme and said lessons had to be learnt from this year's shortages. An extra 200,000 doses of vaccine had been ordered and would be available in the new year, she said. But she sparked a public row with doctors by repeatedly insisting that local GPs were responsible for ordering adequate stocks of vaccines for the annual programme of winter flu jabs, designed to protect millions of elderly people and others deemed at risk from flu.

Ms Hewitt said: "The responsibility for ordering seasonal flu vaccine and the administration of the vaccine has always fallen to GPs - this is a GP-led programme. GPs order their own supply of vaccine based on the number of eligible patients on their register."

She added: "The current problems may be due to a combination of factors, such as under-ordering of vaccine on the one hand, and possibly vaccination of the 'worried well' on the other.

"Awareness may also be higher this year due in part to the very high level of media interest in the threat of avian flu in birds and of pandemic flu."

Doctors rejected Ms Hewitt's statement. Dr Laurence Buckman, deputy chairman of the BMA's GPs committee, said: "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."

Andrew Lansley, the shadow Health Secretary, said ministers had been "grossly negligent". He said the department had added five million carers to the list of at-risk patients entitled to the vaccine this year, but had failed to order adequate stocks of vaccine.

He said the Department of Health had also failed to anticipate a wave of extra demand for the vaccination because of public concern over the threat of bird flu and dramatic warnings of a possible deadly flu pandemic.

He said: "The Government are trying to cover up their own negligence by blaming GPs, and that is a disgrace."

Steve Webb, the Liberal Democrat health spokesman, added: "The department appears to have no clue what is going on. The Department of Health has been grossly complacent about this issue."

The row over the vaccine deepened after it emerged that staff at some government departments had been offered flu jabs. The Treasury and the Home Office confirmed that civil servants had been offered the vaccination. The Foreign Office said London staff had not been given the jab, while the Department of Health itself said only a small number of staff working on critical emergency planning had been vaccinated.

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