Lawrence Area School principal John Auld said 54 pupils - nearly half of the school's roll - were absent on Wednesday with vomiting and diarrhoea.
A lot of pupils had been ill and taken the day off, only to return to school a day later and fall ill again, he said.
"I think it's because of the lousy weather and the kids aren't getting the chance to properly recharge their batteries."
He said illness was also being spread by poor health practices among the children, such as not covering their mouths when sneezing or coughing, and not washing hands properly.
"It's ironic. We're generally a pretty hardy bunch and a bit of flu doesn't normally bother us - we're good, robust country folk."
This week, more than 40 pupils had called in sick each day, but Mr Auld said the number of absentees was beginning to decrease and he hoped the weekend would give many a chance to recover.
Andersons Bay School principal Dave McWhinnie said nearly a quarter of the Dunedin school's population had been ill with a mixture of cold and flu viruses.
"Both the phone lines were ringing red hot with parents calling in to say their children were sick. It has definitely been a bit of an epidemic here."
Two teachers missed work on Monday because of illness and Mr McWhinnie said it had been difficult finding relieving teachers.
Tahuna Normal Intermediate deputy principal Keith Hutton said 142 pupils had been absent for more than one day during the past week.
Many secondary schools were also affected, particularly Otago Girls High School, which had about 140 pupils off sick in the week, and Bayfield High School, which had 70 away at the height of the outbreak.
Mornington Health Centre board of directors chairman Tony Fitchett said there had been an increase in the number of Dunedin residents visiting doctors at the clinic with respiratory illnesses and flu, but he believed the numbers were normal for this time of year.
