Only two-thirds of the population was fully immunised in 2000 against mumps, which is now covered by the measles, mumps and rubella (MMR) vaccine.
Students who haven't had an injection against mumps are being told to stay away from school, even if they miss exams, as Auckland grapples with its worst mumps epidemic in more than 20 years.
St Peter's College principal James Bentley said he had sent a Year 8 student home for 12 days after his family owned up to not being vaccinated, following a case of mumps in the college last week.
The boy will miss end-of-year exams and a Year 8 camp in the Hunua Ranges next week.
Immunisation Advisory Centre director Dr Nikki Turner said about 30 per cent of young people born before 2005, when the national immunisation register started, may not be fully immunised.
A survey in 2000 found that only 68 per cent of the population was fully immunised against mumps, which is now covered by the measles, mumps and rubella (MMR) vaccine given to infants at 15 months.
Turner said some of those who were not vaccinated before 2005 may have had the injection since then, but other young people had come into the country from the Pacific Islands and other countries where there was no routine mumps vaccination.
"It's highly contagious, so if someone has it they are going to spread it," she said.
"The only way to stop it is by vaccinating as many kids as they can."
Auckland Regional Public Health Service clinical director Dr Julia Peters said all "close contacts" of anyone with mumps should stay at home if they have not been vaccinated.
She said 75 per cent of the people who have contracted mumps so far this year had not been vaccinated against it.
"Schools are advised that all students who are diagnosed with mumps are isolated for five days from the first day of swelling in the face, cheek or jaw," she said.
"All the students' close contacts who have not been fully vaccinated or had the mumps illness also need to stay home for 12 days following the first contact with the infected person until 25 days after the last contact with them.
"Staying away from school is needed to stop the spread of the virus further through the school community. It is also protects students and staff who cannot be vaccinated for medical reasons.
"A close contact is considered someone who has spent time with an infected person, and who may have caught the virus by face to face contact within a metre, or sharing objects that may be have been infected."
She said the service had been notified of 839 probable or confirmed cases of mumps this year, including 301 school students across 92 schools.
"We are experiencing Auckland's largest mumps outbreak in over 20 years, and the disease is now well established in communities throughout the region," she said.
"We do not know how many close contacts have been excluded from school as we are not notified of these numbers."
Bentley said the Year 8 student sent home from St Peter's, and the student who contracted mumps who was also in Year 8, would be able to sit exams when they returned to school after other students had sat them.
Meanwhile the grandparents of children at a Waiheke Island primary school have complained that the school has advised pregnant mothers to consider home-schooling their children because of a whooping cough epidemic, even when the children are fully vaccinated.
Te Huruhi School principal Adam Cels said "more than 10" of his 380 students had contracted whooping cough since September, but he denied that he had told families with pregnant mothers to stay home.
"As far as I am aware we have not directly asked people not to come to school (can't speak for all the teachers on this one)," he said by email.
"We have spoken to parents and expecting mums about the dangers of coming into school.
"If children show symptoms we have asked that they be collected from school and suggest they go to the doctor's.
"We have cancelled all meetings this week that involve people from off the island and stopped certain school programmes to try and limit contact with members of our community.