Notices had been sent home to families to ensure children were kept at home if they were unwell.
"It is important that the children don't share their bugs with others by returning to school too soon," she said.
Pembroke School principal Brent Godfery said the school had seen 25 to 40 children, and a few staff members, off school each day in the last week due to illness.
"We've been hit reasonably hard, with about 10 to 15 per cent of kids off school each day," Mr Godfery said.
Waitaki Boys' High School noted a higher-than-normal absentee rate and the boys had been off sick for longer periods this year.
In the past 10 days, St Kevin's College had seen about 50 students become ill, out of a roll of 419, each day.
The illness, which students were taking at least two to three days to recover from, had spread through the St Kevin's Girls' Hostel last week, and was making its way through the Boys' Hostel this week.
With a roll of 210 pupils, Weston School had averaged 20 to 30 absentees each day last week.
Southern District Health Board medical officer of health Derek Bell said it was not surprising to see this pattern.
"Influenza usually affects older and younger people. We have seen some influenza in rest-homes and schools and couple of small rural schools have decided to close for several days - usually because staff are also unwell," Dr Bell said.
