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Just 13% of pregnant women have accepted the offer of a free whooping cough vaccine, figures released by the Ministry of Health show.
In the South, about 19% of pregnant women had had the vaccine since the start of last year, when it was introduced to combat the whooping cough epidemic.
Nationally, more than 9200 women had the free vaccine, up to the end of last month.
Figures were released to the Otago Daily Times after comments at a Southern District Health Board public health committee last week about the problem of low uptake.
Speaking to the committee, public health physician Dr Keith Reid attributed low uptake to a ''deeply ingrained culture'' that a woman was ''inviolable'' during pregnancy.
Vaccination in pregnancy was safe, but it took time to ''break down that culture'' that suggested it might not be a good idea.
''It's a bit of an uphill battle,'' Dr Reid said.
A statement from the Ministry of Health said the most effective way to protect babies before they could be immunised themselves was to vaccinate the mother so antibodies are passed to the baby.
''There is considerable effort made to ensure health professionals are reminding prospective parents about vaccination.
''The vaccine offer to pregnant women at no cost remains in place while the outbreak continues. Once the outbreak ends, the initiative will be reviewed,'' the statement said.
Since the epidemic started in August 2011, New Zealand had had more than 11,200 reported cases, the ministry's website said.
Vaccination sceptic Hilary Butler, of Auckland, believed a maternal instinct to reject vaccination in pregnancy was a good thing.
Her own objection to vaccines was based on published research, she said, but there was a role for instinct and it should not be dismissed.
''Instinct isn't silly; it's there for a good reason.''
Triggering a woman's immune system in pregnancy was contrary to the natural suppression of the immune system during that time, Mrs Butler said.