That equated to an uptake rate of 38.5% – down from 41.4% the previous year.
The NHS recommends that all pregnant women have the flu vaccine, whatever stage of pregnancy they're at, as it will protect both mothers and babies.
The data shows just 37.9% of pregnant women in England got the flu vaccine in 2021-22 – down from 43.6% in 2020-21 and also a record low.
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The UKHSA said delays in GP practices updating records following births or loss of pregnancy means the uptake rate is likely to be an underestimate.
The Royal College of Obstetricians and Gynaecologists (RCOG) said the figures are "concerning".
Dr Pat O’Brien, RCOG vice president, said seasonal flu is an unpredictable virus, and strongly recommended all pregnant women get the vaccine.
He added: "Developing flu during pregnancy can be serious for women and their babies because pregnancy weakens the immune system and results in a greater risk of complications and other infections, such as bronchitis than can develop into pneumonia.
The British Society for Immunology (BSI) said the Government needs to work with the NHS and local authorities to prioritise important immunisation services.
Dr Doug Brown, BSI chief executive, added: "For these initiatives to be successful, we must ensure our immunisation services are properly funded and resourced.”