Only 10.5% of expectant mums in parts of northern England have received the vaccine, latest figures from Public Health England (PHE) show.
Nationally, vaccination rates have fallen by 10 percentage points since February, with only 49.8% of mums-to-be now receiving the pertussis vaccine, Repevax.
Public health chiefs fear the steep fall may leave thousands of newborn infants at risk this winter, a time of year when cases have increased in previous years.
One baby under two months old has already died this year from the disease.
PHE said GP practices and maternity units will be contacted by NHS England teams and urged to improve immunisation rates.
A national pertussis vaccination programme was introduced in October 2012 to protect newborn infants against whooping cough, following an outbreak that began in April 2012.
Vaccinating pregnant women transfers immunity to their unborn child until the first routine dose of the pertussis vaccine can be given at eight weeks old.
PHE experts analysed GP data for 332,594 pregnant women between October 2012 and June 2013. They looked at the proportion of pregnant women due to give birth in each month who had received the pertussis vaccine.
Of the 332,594 women included in the analysis, a total of 175,767 were vaccinated, an average uptake rate of 52.8% over this time. Vaccination reached a peak of 59.6% in February 2013, but fell to 49.8% by June.
In Durham, Darlington and Tees uptake rates fell from 61.5% to 10.5% over this period. In contrast, Devon, Cornwall and Isles of Scilly had the highest vaccination rates in the country in June at 75.9%.
The report said the data should be 'interpreted with caution' due to large variations in the reported number of women between months and areas.
Nevertheless, the authors said the overall fall in uptake was 'of particular concern given that there are still high levels of pertussis activity in the population and a further increase in cases was observed around this time last year'.
RCGP immunisation lead and Berkshire GP Dr George Kassianos said: ‘We need to look into the causes of this relative apathy. Practices should encourage midwives to promote the vaccine to pregnant women. We should write and write again, text and ring every unvaccinated pregnant woman.
'We should never allow another baby to die unprotected when we can protect every single unborn child.’
