In the first six months of 2015 there were 1,744 cases of whopping cough - up from 1,412 in the same period last year.
Only 56.4% of pregnant women were vaccinated in 2014-15, with seven baby deaths from whooping cough in that time.
The vaccine was introduced in 2012 during an increased amount of babies being diagnosed.
Dr Mary Ramsay, PHE's head of immunisation, told the BBC: "It's important that pregnant women visit their GP surgery or midwife to get vaccinated, ideally between weeks 28 and 32 of their pregnancy.
"Being vaccinated against whooping cough while you're pregnant is a highly effective way to protect your baby in the first few weeks of their life."
Public Health England (PHE) said the vaccination reduces the risk of a newborn developing whooping cough by 91%.
A mother who gets the vaccine will produce protective antibodies which are then passed on to the child until they are vaccinated.
Louise Silverton, director for midwifery for the Royal College of Midwives, told HuffPost UK Parents: "This has our support and we echo this appeal for pregnant women to have this vaccine during pregnancy.
"Whooping cough can have fatal consequences for a child and they are particularly vulnerable in the fist two months of life, when they are effectively unprotected against this disease until they have their first vaccination at two months.
"Women must also be aware of the importance of having the seasonal flu vaccination as soon as they become pregnant."
Whooping cough, also called pertussis, is a contagious bacterial infection of the lungs and airways in babies.
The condition begins with a persistent dry and irritating cough that progresses to intense episodes of coughing. It's called whooping cough as the gasping for breath after one of these coughing bouts causes a distinctive noise in the airways.
Other symptoms include a runny nose, raised temperature and vomiting after coughing. The coughing can last for around three months.
Newborns especially are susceptible to getting the infection before they are able to get the vaccination at two months.