Just 63 per cent of the 2,380 women who delivered babies in January had received one dose of the vaccine.
Some 54 per cent had been given two doses, while just 28 per cent had received three.
This reflects a continued trend of pregnant women being less vaccinated than women of a similar age in the general population.
By the end of January, 87 per cent of women aged 18 to 44 had had one dose, while 82 per cent had received two and 57 had three.
The vaccination gap is reducing, PHS said.
Its latest weekly statistical report also found suggestions of worse outcomes for babies in cases where mothers had Covid-19 in the third trimester of pregnancy, which have been raised in previous studies.
The perinatal mortality rate, which includes stillbirths and deaths in the first week of life, remains slightly higher among the 1,265 babies born during the pandemic within 28 days of the mother having Covid-19 compared to the overall rate.
PHS stressed it was not possible to pinpoint Covid-19 as the cause for this.
The rate of premature births is also higher, at 13 per cent in babies whose mothers had Covid in the final month of pregnancy compared to 8 per cent overall in 2019/20.
PHS is conducting ongoing research into the outcomes for mothers and babies of Covid in pregnancy.
The report states: “These detailed analyses aim to provide accurate estimates of any excess risks associated with infection.
"In the meantime, in line with what is known from the international research evidence, the preliminary data presented above suggests that Covid-19 in pregnancy may be associated with an increased risk of perinatal mortality and preterm birth, in particular among babies born shortly after the onset of maternal infection.”
The Joint Committee on Vaccination and Immunisation has included pregnant women as a clinical risk group in the Covid vaccination programme.
Announcing the move last year, Professor Wei Shen Lim, chair of JCVI Covid-19 Immunisation, said: “Women who are pregnant are strongly encouraged to have a first, second or booster vaccine dose as appropriate in order to better protect yourself and your baby.”