A doctor shows how the H1N1 vaccine will be administered. Photograph: Thomas Lohnes/AFP/Getty Images

Family doctors have secured a deal with the government over their payments for giving patients a swine flu jab, it was announced , allowing the final arrangements for vaccination to be put in place.

GPs will be paid £5.25 for each jab they give. The wrangle over payments has been going on all summer. Doctors represented by the British Medical Association appear to have reduced their demands from an initial level of almost £7 a shot. They are paid £7.50 a patient to give the seasonal flu vaccine.

Although the government has ordered enough vaccine for the entire population, the vaccination programme expected to begin in the autumn – once the vaccine receives a licence – will target the 9 million people most at risk from swine flu, the government said today.

Whether the rest of the population is then offered a jab will depend on the evolution of the pandemic, it said. If it continues to be mild, vaccination will not be introduced universally.

GPs stand to gain more than £42m, which they say will be spent on contacting patients, administering the vaccine and if necessary taking on extra staff. A statement from the Department of Health noted that "the vaccine will reduce the number of people needing hospital and intensive care treatment and save the NHS money in the long run".

The health secretary, Andy Burnham, said the deal was "great news for patients". He added: "I am glad that we have reached a fair deal with the GPC [general practitioners' committee of the BMA] and I am pleased that GPs will continue to play a key role in the fight against swine flu. They have already worked incredibly hard in what have been very difficult circumstances to help their patients."

Dr Laurence Buckman, chairman of the GPs' committee, said it believed family doctors were the best people to administer the vaccine. "This will be a lot of additional work for practices, but general practice is used to running large vaccination programmes. We are confident that GPs and their teams will have the resources they need in order to run the swine flu vaccination programme smoothly and efficiently." Four groups of people were identified as the first who will be summoned for a flu jab in England:

• People aged over six months and under 65 who are currently considered to be at risk from normal winter flu because of health conditions such as asthma or heart conditions ‑ about 5 million people.

• All pregnant women, unless the regulatory authorities impose restrictions on the stage of pregnancy in which it is safe to vaccinate ‑ about 500,000.

• Household contacts of people with compromised immune systems, such as people in regular close contact with patients on treatment for cancer ‑ about 500,000.

• People aged 65 and over in the current seasonal flu vaccine clinical at-risk groups ‑ about 3.5 million. This does not include otherwise healthy over-65s, since they appear to have some natural immunity to the virus.

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