Uptake of 50.7 per cent is required for the thresholds of the patient experience indicators in the QOF to be lowered for 2009/10 under the deal agreed between the BMA and NHS Employers.
Just 39 per cent of those in at-risk groups and 22 per cent of pregnant women have been vaccinated. Only 8 per cent of healthy children have been vaccinated, but the national agreement on payment for swine flu jabs did not include this group.
The DoH says vaccination remains important, with swine flu continuing to cause deaths and critical care admissions, although case numbers are low.
England's CMO Sir Liam Donaldson said that although swine flu has not been a severe illness for most people, children and younger adults have developed serious complications.
'When the virus returns in the 2010 flu season those who develop complications or die will be doing so from a vaccine preventable disease,' he said. He urged eligible patients to have the jab.
Meanwhile, Health Protection Agency data shows case numbers among children and young people are 10 times higher in high-risk areas of England than original estimates suggested.
Writing in The Lancet, researchers said infection rates were greatest in school children aged 5-14 years, with an estimated 42 per cent infected in high incidence regions.