The vaccine is available to all mothers-to-be in Scotland at any point during their pregnancy from October to March.
However, there is ongoing concern among doctors that many are not taking up the option, which helps protect their babies.
Gillian Smith, director for Scotland at the Royal College of Midwives, said after the release of disappointing statistics: "It is really important that pregnant women do get their flu vaccine and that midwives encourage them to do that.
"Women should be aware of the importance of having the seasonal flu vaccine as soon as they become pregnant. If any pregnant woman is unsure about this it is crucial they speak to their midwife or doctor. Don't leave it too late."
Government figures show only 48% of expectant mothers were immunised last year, compared to 53% for the previous year. It comes despite various campaigns aimed at encouraging women to "get a shot" of the vaccine.
Only 65% of the pregnant women considered to be at risk took up the vaccine in 2013/14, down from 68.7% the year before.
The flu vaccine protects mothers against getting flu but will also protect babies for several months after their birth.
Public Health Minister Michael Matheson urged all women to strongly consider getting the vaccine if they become pregnant.
He said: "It goes without saying that all women want to do as much as they can to keep their baby safe and healthy during pregnancy, which is why it's concerning that less than half of mums-to-be were immunised this winter.
"The flu vaccine is safe and effective, and offers protection to both mother and baby. The Royal College of Midwives and Scotland's Chief Medical and Chief Nursing Officers have all stated that the flu vaccine will protect both mother and baby at what is an extremely vulnerable time.
"The flu vaccine cannot give you flu and all the experts agree on this. Not having the vaccine simply isn't worth the risk, for you or your baby."
The flu vaccination is available for free to people aged 65 and over, those under 65 with a condition that puts them at greater risk, pregnant women, unpaid carers and health workers.
The Government statistics showed there was an increase in the number of at-risk under-65s getting the vaccine and 76.9% of those over-65 were getting it - above the World Health Organisation's target of 75%.
Among those who have taken part in awareness campaigns is Scotland and Celtic striker Suzanne Grant.
Ms Grant has spoken of how she was vaccinated before giving birth to her baby son.
She has pointed out how easy it is to get the jab and the peace of mind benefits it brings for mothers-to-be.