Some 78% of women who gave birth at the end of January were found to have received the safeguard, which protects the newborn from whooping cough in the first few weeks of life.
The immunisation was introduced by NHS Scotland in September, given rising rates of whooping cough – bordetella pertussis – with 1923 confirmed cases in 2012, around 10 times the rate in 2011.
The take-up rate is considered high but the Scottish Government and a leading child welfare group have urged all mothers-to-be to be vaccinated. There is no known specific reason why the other 22% have not had the vaccination.
A spokeswoman for Children1st said: "It's encouraging to see that take-up rates of the new vaccination for pregnant women against whooping cough are so high. However, this still means that one in five women isn't taking up the vaccine.
"We would urge mums-to-be to take up this protection for their newborn babies: whooping cough is on the rise and can be very serious for young babies."
Young infants are most severely affected by the highly infectious bacterium and are more likely to develop complications and require hospital treatment.
Following birth, the jab will routinely be offered to newborns once they are old enough to qualify for the childhood immunisation programme at eight weeks old.
Infection rates appear to remain high. with 223 confirmed cases of whooping cough in the first five weeks of 2013.