A free whooping cough vaccine is now available to all pregnant women.
The vaccine protects newborn babies from the disease, which is also known as pertussis.
In just over three months, the Southern District Health Board had 97 cases reported and there were 214 reported in the past year.
Public Health South public health physician Dr Keith Reid said a current epidemic began in the early spring of 2011.
"One of the reasons we are seeing increased numbers of cases is because the immunity to the infection decreases with age and this means that older people, who previously were immune to pertussis, are now getting infected and helping to spread the infection around the community," he said.
Dr Reid said the Southern DHB area had a higher than expected rate of cases, but had not seen the localised outbreaks that had occurred in other parts of the country.
Pertussis is a disease that has the biggest impact on newborns and infants under 1 year of age because they typically lack immunity to the infection. Nearly half of those under 1 year of age with pertussis will be in hospital as a consequence of the infection.
Vaccination is the single most effective measure to tackle the spread of the infection and it is important that infants are presented for vaccination at the appropriate times; at ages 6 weeks, 3 months and 5 months. Boosters are usually given at age 4 years and 11 years.
Pregnant mothers are recommended to receive the funded vaccination between 28 and 38 weeks.
Plunket southern clinical adviser Maxine Wilkins said pertussis begins with a cold-like illness with a runny nose.
"Pertussis is most infectious in the early stages so at the moment with higher than expected levels of the infection in circulation it is important for parents of infants or children who have developed a cough and who may have been in contact with other cases to get attention from their general practitioner," she said.
Health Minister Tony Ryall said research showed the most effective way to protect babies before they were immunised was to vaccinate the mother during pregnancy.
"Whooping cough is a very contagious disease. Figures show that 70 per cent of babies who contract the disease in the first few weeks of life, catch it from their parents or other close family members," he said.
The free Boostrix vaccine is available from GPs.