Figures show uptake of the seasonal jab among people over 65 years was 47.5% in the year to October. By this time last year, uptake had reached 54.4%.
Just 26.3% of people aged under 65 in a risk group have been vaccinated, compared to 31.1 by this time last year.
The department said the 'blip' in uptake could be explained by a period of milder than usual weather for this time of year or it could be due to people being unnecessarily concerned about the jab containing swine flu vaccine.
Professor David Salisbury, director of immunisation has written to health bodies and professionals asking them to increase efforts to improve uptake rates.
‘It is important that trusts work with their GPs and other providers in order to encourage more eligible people to come forward for vaccination,’ he said.
Previously, GP reported that the GMC advised GPs to alert patients who refused last year's swine flu vaccine that it is included in this year's seasonal flu jab.
At the time, GPC negotiator Dr Peter Holden said 'there is always the possibility' vaccine uptake could be hit, although any fears over the vaccine were unfounded.