East Otago High School principal Rick Geerlofs said his school continued to be hit hard by winter bugs, and on two days last week, about a quarter of the school's pupils were absent through illness.
"The flu has hit with a vengeance."
In a recent school newsletter, Mr Geerlofs advised parents to monitor their children's health closely and if they were unwell, they should be kept at home.
"It is, in fact, probably better to keep them at home, rather than have the germs spread through the school."
Mr Geerlofs said flu epidemics seemed to hit schools once every five to 10 years, but this year was one of the worst for absences that he could recall.
While the majority of those pupils taken ill were on the mend, several staff members were now coming down with flu. He assured the community the running of the school would not be compromised.
"This is just a blip on the radar."
Otago Secondary Principals Association chairman and Kaikorai Valley College principal Philip Craigie said of the 800 pupils at his school, up to 200 were absent with illness at the height of the flu epidemic last term.
However, the recent school holidays had helped pupils recover and stamp out the winter bugs.
"Compared with this time last year, we are healthier - there are far fewer people away. Touch wood, I hope it stays this way for the rest of the winter."
Kavanagh College principal Paul Ferris said he also had noticed an improvement in the health of his pupils.
"The barometer is we don't have any coughing or sneezing in assemblies at the moment.
"There was a prediction that 50% of staff and pupils would be away sick, due to the H1N1 virus, and we were required to have pandemic plans in place.
"We haven't been affected in the way we thought we would."
The majority of schools in Otago reported improvements in the health of their pupils and Mr Craigie believed the holiday period and sunnier weather during the past month were contributing factors.
