The number of over-65s, under-65s with an underlying medical condition, and pregnant women receiving a flu jab at this time in 2018 has fallen compared to 2017, Public Health England (PHE) said.
The dwindling number of patients who received their flu jab comes after concerns were raised about the way the vaccine was distributed this year.
GPs were reportedly turning patients away after receiving their stock in a phased distribution.
Health officials said that the manufacturer Seqirus, the sole supplier of the new vaccine for over-65s, phased deliveries to cope with global demand.
But some medics raised concerns over such deliveries, saying they would run out between batches.
Last month NHS England issued reassurances that all vaccines have now been delivered as ordered.
Figures from PHE show that flu vaccine uptake up to week 48 in 2018 for over-65s was 65.4 per cent, compared to 69.1 per cent in 2017.
Uptake for pregnant women was 40.8 per cent for the period in 2018, down from 43.1 per cent in 2017.
The uptake for under-65s in a clinical risk group was 43.5 per cent for the period in 2017, higher than the 40.7 per cent in 2018.
PHE said early indications suggest that the predominant strain of flu circulating this year is Influenza A (H1N1pdm09), commonly called "swine flu", which is well-matched to the strains in this year's flu vaccines.
The health body is urging anyone who is eligible to take up the offer of the free flu vaccine in the next few weeks, ahead of when flu typically starts to circulate in late December and when people start to mingle over the Christmas period.
Professor Paul Cosford, medical director for Public Health England, said: "It is even more important than ever that all those eligible take up the offer of the flu vaccine, especially before Christmas when many people will be gathering together with the added risk of spreading infection that this brings."