PCTs had hoped to capitalise on swine flu fears by increasing uptake of seasonal flu jabs.
Many aimed for uptake levels as much as 5 per cent above the WHO target of 75 per cent among over 65-year-olds.
Some also increased vaccine orders to cope with a rise in demand, to cover PCT staff vaccinations and help GP practices facing stock shortages.
But responses to a freedom of information request show that, of 49 PCTs aiming to achieve uptake rates above WHO targets, just 11 succeeded.
In addition, among 30 PCTs that aimed to achieve uptake rates above WHO targets for under 65-year-olds in at-risk groups, just 13 hit their targets.
Across England, uptake of seasonal flu jabs among over- 65-year-olds fell to 72.4 per cent in the last flu season, from 74.1 per cent the year before. In 2009/10, uptake in over-65s slowed between October and November.
'The change in uptake rate between 2008/9 and 2009/10 may have been due in part to the introduction of the H1N1 influenza pandemic vaccination programme, which started in October 2009,' the DoH said.
The DoH is now examining the effect of swine flu on seasonal flu uptake and looking at whether there were geographical variations in this effect.
The DoH has warned that many at-risk patients remain unvaccinated.