Dr. Lamont Sweet said there have been six confirmed cases of the highly contagious infection in the province since December.
He said the affected patients are between the ages of seven weeks and 20 years old.
Sweet said two of the six confirmed cases resulted in hospitalization, but one person has since been released. He did not know the age of the patient who remains in hospital, and could not comment specifically on their condition.
"We haven't had any recent update of alarm," he said. "We've had no deaths."
The patients are being treated with antibiotics, which Sweet said would help prevent the illness from spreading but not stop the cough. He said the illness can take between six and 12 weeks to run its course.
On average, Sweet said the province has seen only one case of whooping cough a year over the past nine years.
Sweet said some of the patients affected by the outbreak were immunized against whooping cough, while others weren't.
"In the rest of the country there have been frequent outbreaks and there's been many in the United States," he said. "The vaccine is much, much better than it used to be, but it's not 100 per cent preventative."
Last year, a government study released in the U.S. suggested that the vaccine may keep people from getting sick but not necessarily prevent whooping cough from being spread to others.
In 2012, New Brunswick experienced its largest ever outbreak of whooping cough after more than 1,400 cases were reported, mostly children from 10 to 14 years of age.
Whooping cough, also known as pertussis, infects the respiratory tract and is spread by a bacterium. Symptoms include fever, vomiting and coughing attacks that worsen over time and end with a characteristic whooping sound. It can be particularly problematic for infants.
Complications listed on the Public Health Agency of Canada's website include pneumonia, seizures, brain damage and death.