NZ child hospital admission rates for the disease are around three-fold higher than in Australia and the United States.
The Immunisation Advisory Centre at Auckland University says vaccinating pregnant women causes a rise in antibodies against the whooping cough bacterium. The antibodies cross the placenta into the baby and can provide protection against the disease until the child receives its own vaccinations.
Last year 990 cases of whooping cough were reported nationally from January to November, down from 1080 for the same period in 2015.
In the study by the Auckland and Otago universities, 37 women with infants were recruited in pharmacies and interviewed about why they did or didn't receive the vaccine during pregnancy.
Seventeen of the women did receive the vaccine against whooping cough, also called pertussis, during pregnancy.
"About one-third of respondents could not recall any discussion about pertussis vaccination during pregnancy," says the research paper, published in the Journal of Primary Care.
Other reasons for not being vaccinated were concerns about safety and misinformation.
The College of Midwives said it encourages members to tell pregnant women about the free vaccination scheme.
One of the researchers, Crystal Braganza, said the interviewees were "very supportive of having the whooping cough vaccine available free in pharmacies.
"They thought it would help get the message out to pregnant women and would be convenient to access."
Immunisation Advisory Centre research director Dr Helen Petousis-Harris said New Zealand's uptake of the vaccine during pregnancy was uncertain. There had been local initiatives before the national scheme started, such as in Canterbury, where the uptake had been considerably higher than the rest of the country for a time.
"By focusing on pharmacies we can increase awareness and make it easy for people."
A vaccine recipient
Katrina Broughton had a whooping cough vaccination when she was 32 weeks through her pregnancy with son, Ezra.
"It was a no-brainer, especially with the prevalence of whooping cough," said the Auckland University project analyst and accountant, whose son is now 14 months old.
"There was a video out of Waikato of a baby who had whooping cough in hospital and was struggling to breathe.
"You want to do everything you can to protect your child. When I went to see my obstetricians they mentioned it as well as my GP."
She receive the injection from a nurse at her GP's clinic.
Broughton understood that all of the pregnant women she met while carrying Ezra had received the injections, too, but said they were probably not representative of the whole New Zealand population and more needed to be done to promote whooping cough vaccination for expectant mums.
"I think before I started working at the university I wasn't aware that whooping cough is such an issue."
She said some women might find pharmacy vaccination against whooping cough more convenient, although many wouldn't need it.
"You are either going to your GP or in constant contact with a midwife or obstetrician. If one of those three can give it to you while you're pregnant, you wouldn't necessarily need to go to a pharmacist to get it done."