Roslyn Pharmacy owner Andrew Hou said traditionally "one or two" people would visit the pharmacy for the vaccine about this time of the year, but since the report of the two infections, it had been "mayhem".
"It’s definitely going out the door. We ran out yesterday and we're likely to run out again this morning."
He advised people living in close-quarter residences such as student halls or military barracks to apply for the vaccine, as it was subsidised in those cases.
Everyone else needed to be alert and get the vaccine if they were concerned, particularly students in flatting arrangements.
"It’s really quite serious."
Pharmacist Kate Catchpole said they were ordering "about 10 boxes at a time" of the two main vaccines and these were all picked up before the day’s end.
"I think just ringing your pharmacy to make sure they have the stock is probably a great idea."
Albany Street Pharmacy's Greg Andrews also reported strong demand for the vaccine yesterday.
National Public Health Service medical officer of health Dr Michael Butchard said there had been two reported cases of the virus in Dunedin over the past week.
"The National Public Health Service in Southern are treating these cases as a meningococcal outbreak in Dunedin.
"Meningococcal bacteria do not spread as easily from person-to-person as infections like measles or the flu. The risk of meningococcal disease in the community or among other students and staff remains low, as the infection is only passed on when people have close or prolonged contact with a case."
Despite the demand for the vaccine, Health New Zealand confirmed there was no issue with vaccine supply in New Zealand.
"Pharmac are ensuring there is adequate supply of the MenACWY and MenB vaccines available in Dunedin," a spokesman said.
